8 Best Healthcare Payment Processors
Healthcare practices need payment processors that are secure, HIPAA-compliant, and easy for patients to use, whether they pay in person, online, or through a portal. Many standard payment processors don’t meet these requirements, which can lead to compliance risks or extra administrative work.
To help small and new practices choose the right solution, we evaluated top healthcare payment processors based on HIPAA compliance, pricing, EHR integrations, payment methods, and ease of use.
These are the eight best healthcare payment processors and what each one is best for:
The Health Insurance Portability and Accountability Act (HIPAA) sets standards for how healthcare organizations store, transmit, and protect protected health information (PHI). PHI includes any information that identifies a patient and relates to their health, treatment, or payment for healthcare services.
Examples include:
- A patient’s name linked to an appointment or invoice
- Diagnoses, treatment notes, or medical history
- Insurance details and explanations of benefits
- Payment records tied to a patient’s identity
💡Credit card processing alone is not a HIPAA-covered activity
If a processor only handles the technical act of running a card and does not store patient information, invoices, clinical details, or appointment data, HIPAA does not apply. This is because banks and card networks operate under a regulatory exemption.
However, many modern payment processors offer features that do involve PHI, such as:
- Invoicing and billing
- Card-on-file storage
- Recurring payments
- Appointment scheduling
- Patient portals and payment plans
Once a processor stores or displays patient-identifiable information, HIPAA becomes mandatory.
What makes a payment processor HIPAA-compliant?
A processor is considered HIPAA-compliant only if it does BOTH of the following:
- Signs a Business Associate Agreement (BAA): A BAA utlines how patient data is protected, used, and secured. Without a BAA, a processor cannot legally store or access PHI for a healthcare practice.
- Uses HIPAA-compliant systems for storing or transmitting PHI: This includes secure patient portals, billing platforms, invoicing systems, and tools like InstaMed or Salucro.
💡PCI compliance is not the same as HIPAA compliance
Many processors advertise PCI Level 1 certification. PCI protects cardholder data, not patient health information. PCI compliance indicates strong payment security, but it does not replace HIPAA requirements or allow a processor to store PHI without a BAA.
HIPAA requirements for payment tools
Top healthcare payment processors compared
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How I chose the best healthcare payment processors
To evaluate the best healthcare payment processors for small businesses, I fact-checked each provider to ensure that pricing and features were accurate. I then scored each one on 20 data points, prioritizing value for money and ease of use. See my full methodology below.
I have over five years of experience testing and reviewing payment processing technology, merchant services, and POS systems. My goal is to help small businesses streamline financial workflows and boost efficiency.
Payments Staff Writer at Fit Small Business
Improve your security and workflows with our top recommendations:
Square: Best fully HIPAA-compliant free merchant account
Pros
- Fully HIPAA-compliant with BAA
- Free invoicing, recurring billing, and website builder
- Accepts HSA/FSA cards
- Multiple EHR integrations
- Waived chargeback fees
Cons
- Support limited to extended business hours
- Same-day deposits require a fee
- Account stability issues for some users
Overview
Who should use it:
Small and new healthcare practices needing a free, HIPAA-compliant payment system with online and in-person tools
Why I like Square Payments:
Square is one of the few widely used payment processors that is fully HIPAA-compliant and willing to sign a Business Associate Agreement (BAA), making it safe for storing patient-identifiable billing information. It offers free invoicing, recurring billing, online checkout, and a basic appointments POS, which are features that many competitors charge extra for.
Practices automatically get support for HSA and FSA debit cards and can start accepting payments almost immediately after sign-up. Square does not require long-term contracts, monthly fees for payment processing, or underwriting for most small practices, which keeps the onboarding process simple and accessible.
- Monthly fee: $0 to $149
- In-person transaction fee: 2.6% + 15 cents
- Invoicing: 3.3% + 30 cents
- Online transaction fee: 2.9% + 30 cents
- Recurring billing and card-on-file: 3.5% + 15 cents
- Keyed-in/Virtual terminal payments: 3.5% + 15 cents
- ACH/Bank transfers: 1% ($1 min)
- Chargeback fee: Waived up to $250 per month
- Full HIPAA compliance
- Integrates with Remedly and DrChrono EHR platforms
- Accepts HSA and FSA debit card payments
- Free aggregate merchant account
- Free basic appointment POS software and website builder
- Free invoicing and recurring billing
- Includes ACH payment processing
- Free next-day funding, same-day funding with fee
Square is an excellent choice for small and startup healthcare organizations. It even offers volume discounts for merchants that process more than $250,000 per year. However, Square’s customer support is also limited to extended business hours. There are also merchant service providers that can offer better interchange rates for fast-growing healthcare organizations.
Related reading:
PaymentCloud: Best for healthcare practices classified as high-risk
Pros
- 98% approval rate for high-risk merchant accounts
- Fully HIPAA-compliant with BAA
- Extensive payment gateway and EHR integrations
- Dedicated account manager
- Next-day funding available
Cons
- Pricing is not publicly disclosed
- Virtual terminal and gateway often require added monthly fees
- Longer underwriting process than instant-approval processors
Overview
Who should use it:
Telehealth, subscription-based, mobile, or other high-risk healthcare practices that need HIPAA compliance and strong approval odds
Why I like PaymentCloud:
PaymentCloud specializes in industries that traditional processors classify as high-risk, including telehealth, mental health, medical subscriptions, concierge care, supplement sales, and online-first practices. With multiple acquiring bank partners and a 98% approval rate, it’s one of the most reliable ways for high-risk healthcare organizations to secure a HIPAA-compliant merchant account.
PaymentCloud signs BAAs, offers extensive fraud prevention tools, and supports a wide range of payment methods. Its integration ecosystem is large, including compatibility with many EHR and billing platforms through gateways like Authorize.net and NMI. Each healthcare client is also assigned a dedicated account manager, which helps streamline onboarding and ongoing support.
Learn more: Best high-risk merchant account providers
- Monthly fee: $10 to $45*
- Payment gateway fee: $15 per month (average)
- Virtual terminal: $15 to $45 per month
- Transaction fees:
- Low-risk: 2% to 3.1%
- Medium-risk: 2.3% to 3.4%
- High-risk: 2.7% to 4.3%
- Chargeback fee: $25
- Early termination fee: Waived
*Rates vary among industries and clients. Pricing is based on average mid- and high-risk merchant services.
- Fully HIPAA-compliant with signed BAA
- Thousands of direct integrations, including EHRs
- Low monthly fees for high-risk merchant accounts
- Flexible transaction fee pricing
- Accepts HSA and FSA debit card payments
- Accepts e-check payments
- Advanced fraud prevention tools
- Can reprogram compatible existing hardware
- 24/7 customer support
PaymentCloud is particularly strong for telehealth, online, and membership-based practices that may struggle to get approved elsewhere. While pricing is less transparent and onboarding can take longer, its compliance readiness, broad integrations, and high-touch support make it one of the most reliable options for high-risk healthcare businesses.
Some healthcare practices can use an international merchant account instead of a high-risk merchant account.
Online healthcare services are primarily considered high-risk. However, if you’re not keen about the extra work and fees associated with a high-risk merchant account, an international merchant account for your healthcare practice can be a good alternative.
An international merchant account is great for:
- Practices that attend regularly to tourists: You can accept various international credit and debit cards and even local payment methods from different countries.
- Large practices with international locations: You can manage all your payments from a single merchant account platform.
This is where doing your research on multiple merchant account providers plays an important role. See our top picks for international merchant accounts.
Chase Payment Solutions: Best for healthcare practices using InstaMed
Pros
- Free same-day funding with Chase Business Checking
- Native integration with InstaMed
- Fully HIPAA-compliant billing and payment workflows
- No long-term contracts
- 24/7 customer support
Cons
- Hardware must be purchased upfront
- Monthly fees may apply for InstaMed services
- Chargeback fees are not refundable
Overview
Who should use it:
Healthcare practices using InstaMed or needing a bank-backed, HIPAA-compliant billing and payment platform
Why I like Chase:
Chase owns InstaMed, one of the most widely used HIPAA-compliant billing and payment networks in healthcare. More than half of US healthcare providers use InstaMed to manage patient payments, statements, claim remittances, and online billing. By connecting Chase Payment Solutions with InstaMed, practices gain a fully HIPAA-compliant environment without needing multiple vendors.
Chase also stands out with free same-day funding when deposits go into a Chase Business Checking account — an advantage for clinics with tight cash flow. Its flat-rate pricing is transparent, hardware can often be reprogrammed, and the platform integrates with nearly any EHR through InstaMed’s established partner network.
- Monthly fee: $0 to $15*
- In-person transaction fee: 2.6% + 10 cents
- Online transaction fee: 2.9% + 25 cents
- Keyed-in transaction fee: 3.5% + 10 cents
- ACH processing fee: $25 per month for 25 transactions, 15 cents for additional
- Chargeback fee: $25 to $100
*Merchants with a Chase Business Checking account are required to maintain a minimum balance of $2,000 or a monthly service fee of $15 will be imposed.
- Fully HIPAA-compliant when used via InstaMed
- Accepts HSA and FSA debit card payments
- Accepts ACH payments
- Automated payment processing and reconciliation
- Free traditional merchant account
- Free same-day funding
- Can reprogram compatible existing hardware
- 24/7 customer support
Chase is an excellent option for practices already using InstaMed or those wanting a unified, HIPAA-compliant billing platform backed by a major bank. While it’s not as plug-and-play as Square, its healthcare-specific infrastructure and funding speeds make it ideal for larger or more established practices.
However, if you want Chase for its free same-day funding feature, you will need to open a Chase Business Checking account and maintain a minimum balance of $2,000 per month.
How to add a real-time payment method for your healthcare practice
Some practices may require regular fast access to funds to improve cash flow. In cases like this, it’s impractical to keep paying add-on fees just to get same-day funding. Instead consider working with traditional banks like Chase and US Bank (also included in this list) that offer direct payments in 2 ways:
- Real-time payments (RTP): Both Chase and US Bank are members of FedNow service that supports instant bank-to-bank transactions.
- Via Zelle: Both Chase and US Bank are in the Zelle network of bank partners so patients with a Zelle account can pay you instantly via the Zelle platform.
Learn more about real-time payments.
Dharma Merchant Services: Best low-cost credit card processing for midsize healthcare providers
Pros
- Fully HIPAA-compliant with BAA
- Low interchange-plus pricing
- Next-day funding for card-present transactions
- Multiple EHR integrations
- Excellent customer support
Cons
- Monthly fee and additional charges for ACH and invoicing
- Surcharge for Amex transactions
- PCI non-compliance fee
- One-year contract
Overview
Who should use it:
Midsize healthcare practices that want low-cost interchange-plus pricing and can manage a few add-on fees
Why I like Dharma Merchant Services:
Dharma offers some of the most competitive interchange-plus pricing available to healthcare providers. Because Dharma is fully HIPAA-compliant and willing to sign a BAA, practices can safely use its invoicing, recurring billing, virtual terminal, and reporting tools without compliance concerns.
Unlike many payment aggregators, Dharma provides a dedicated merchant account, which reduces the risk of frozen funds and improves stability for growing clinics. Its pricing transparency is also a standout — rates are easy to understand, with no long-term contracts beyond a standard one-year agreement.
Dharma integrates with a wide range of EHR and practice management systems, making it a strong fit for clinics that already have established software workflows and want predictable, low-cost processing.
- Monthly account fee: $25
- Transaction fee: Interchange plus 0.15% + 8 cents
- Amex transaction fee: Interchange plus 0.25% + 8 cents
- High-volume transaction fee: Interchange plus 0.10% + 8 cents*
- ACH monthly fee: $25 + 40 cents per transaction
- Invoicing and recurring billing monthly fee: $10
- Chargeback fee: $25
- Account closure fee: $49
*For sales volume above $100,000 per month
- Fully HIPAA-compliant merchant account
- Likely integrates with most EHR systems
- Accepts FSA and HSA debit cards
- Free virtual terminal
- Free mobile POS app
- Compatible with Clover hardware
- Guaranteed 48-hour funding
- Next-day funding for card-present transactions
Dharma Merchant Services can integrate with any EHR system with a signed BAA, but still consult with a Dharma representative to verify that it will work with your current healthcare service management system. Even with a fully HIPAA-compliant merchant account service, Dharma’s ranking in our evaluation was significantly affected by the potential add-on fees, including incidentals such as PCI non-compliance and account closure.
Stax: Best for high-volume healthcare practices
Pros
- Wholesale interchange-plus pricing
- No cancellation fees
- Wide range of payment and billing tools
- 24/7 customer support
- Volume-friendly pricing structure
Cons
- Not HIPAA-compliant; no BAA available
- High monthly subscription cost
- No same-day funding option
- Requires Zapier/API for EHR integrations
Overview
Who should use it:
Established, high-volume healthcare practices that only need card payment processing and want to reduce processing costs
Why I like Stax:
Stax is one of the few payment processors offering true wholesale interchange pricing, which can significantly reduce costs for practices processing $20,000 or more per month in card payments. The platform includes robust invoicing, reporting, and billing tools at no additional transaction markup, which are features that typically require add-on fees elsewhere.
However, Stax does not sign BAAs and should not be used for workflows that involve PHI, including patient invoicing, recurring billing tied to patient data, or EHR-integrated payment collection. For practices that strictly need a pricing-efficient card processor for front-desk transactions, Stax can offer strong savings.
- Monthly fee: $99 to $199
- Card-present transaction fee: Interchange plus 8 cents
- Card-not-present transaction fee: Interchange plus 18 cents
- Chargeback fee: $25
- PCI Level 1 security compliance
- Integrates with Aesthetics EMR via Zapier
- Integrates with other EHRs via API
- Accepts HSA and FSA debit cards
- Wholesale interchange-plus pricing
- All-in-one monthly fee for all payment types
- Next-day funding option
- 24/7 customer support
Stax is best suited for high-volume practices that want to optimize card payment costs and do not need HIPAA-compliant billing or EHR-integrated payment features. Smaller clinics or those requiring PHI-related workflows will be better served by HIPAA-compliant providers like Square, Chase (InstaMed), or PaymentCloud.
Ivy Pay: Best for small therapy practices
Pros
- Fully HIPAA-compliant
- No monthly fees
- Mobile app works on iOS and Android
- Very simple setup
- Accepts HSA/FSA cards
Cons
- Limited to therapists using Talk to Ivy
- Minimal integrations; not a full practice management system
- Limited notification and customization options
Overview
Who should use it:
Solo therapists or small therapy groups needing a simple, mobile-based HIPAA-compliant payment solution with no monthly fees
Why I like Ivy Pay:
Ivy Pay is built specifically for behavioral health providers and offers one of the simplest onboarding experiences in the industry. Therapists download the mobile app, link a bank account, and can immediately begin accepting patient payments. The platform is fully HIPAA-compliant, supports HSA and FSA debit cards, stores cards on file, and deposits funds the next day.
Where Ivy Pay stands out is ease of use: it removes the complexity found in full medical billing systems and focuses solely on fast, secure payments. This makes it ideal for therapists who manage their own billing or operate part-time practices.
However, Ivy Pay offers limited integrations and is tied closely to the Talk to Ivy referral service, which may make it less suitable for larger clinics or multidisciplinary practices.
- Monthly fee: $0
- Transaction fee: 2.75%
- Cancellation fee: $0
- Fully HIPAA-compliant
- Built-in payment processor for Talk to Ivy referral services platform
- Mobile-based, remote payment processing
- Accepts HSA and FSA payments
- No long-term contracts
- No credit card reader required
Ivy Pay is an excellent choice for therapists who want a HIPAA-compliant payment tool without the overhead of a full POS or billing system. While too limited for most clinics, it fits perfectly for solo and small therapy practices.
U.S. Bank Merchant Services: Best for healthcare practices using Salucro
Pros
- Fully HIPAA-compliant via Salucro
- Free same-day funding
- Supports ACH, HSA/FSA cards, and patient payment portals
- No long-term contracts (even with hardware rentals)
- 24/7 customer support
Cons
- Monthly account fees for many plans
- Hardware rental adds ongoing cost
- Integrations not clearly listed
- Setup fee may apply
Overview
Who should use it:
Healthcare practices that integrate their EHR systems with Salucro for invoice and billing management
Why I like U.S. Bank Merchant Services:
U.S. Bank Merchant Services is one of the few major banks offering a HIPAA-compliant payment workflow through its integration with Salucro, a widely adopted healthcare billing and payment platform. Salucro supports patient portals, online payments, ACH, HSA/FSA cards, text-to-pay, and even remote check deposit, giving healthcare organizations a unified system for collecting patient balances.
Practices that maintain a U.S. Bank business account also benefit from free same-day funding, a valuable feature for clinics with high daily volumes or tight reimbursement cycles. In addition, the ability to rent hardware (without long-term contracts) makes it easier for practices to scale up or down their in-office payment options.
While its pricing structure is less transparent than Square or Helcim, U.S. Bank’s integration with Salucro and its bank-backed reliability make it a strong fit for mid- to large-size medical practices already steeped in Salucro’s ecosystem.
- Monthly fee: $0 to $99
- In-person transactions: 2.6% + 10 cents
- Keyed-in transactions: 3.5% + 15 cents
- Online transactions: 2.9% + 30 cents
- Online ordering: $0 to $49 per month
- Hardware: $20 per month to $34 per month + $4.95 insurance fee
- Setup fee: $0 to $99
- Fully HIPAA-compliant with Salucro
- No long-term contracts even with hardware rental
- Accepts HSA/FSA cards, ACH, and remote check deposits
- Mobile, online, and invoicing tools
- Patient-facing payment portal
- Option to rent card readers and payment terminals
- Free same-day funding
- 24/7 customer support
- Free surcharging and debit card optimization
U.S. Bank Merchant Services is an excellent fit for practices that rely on Salucro for patient billing or want a bank-backed processor with strong healthcare capabilities. Small practices that don’t need Salucro’s billing infrastructure may find providers like Square or PaymentCloud more cost-effective.
Limited-time offer: Earn a $400 statement credit when you process at least $5,000 in transactions within 60 days of approval of your new U.S. Bank Payment Solutions account. Member FDIC.
To qualify, you must (1) open and be approved for a U.S Bank Payment Solutions Merchant Account (MID) between April 1 and June 30, 2026, (2) process at least $5,000 in transactions within 60 days of approval, and (3) keep the approved account in an open status and be actively accepting and settling card payments at the time the statement credit is issued.
Helcim: Best for free HIPAA-compliant invoicing and billing services
Pros
- Fully HIPAA-compliant with BAA
- No monthly fees
- Free invoicing, recurring billing, and virtual terminal
- Interchange-plus pricing with automated volume discounts
- Level 2/3 data optimization
Cons
- Higher-priced hardware compared with other providers
- Limited EHR integrations (mostly custom/API)
- Slower funding times for some merchants
- No built-in patient portal
Overview
Who should use it:
Growing healthcare practices that want low-cost, HIPAA-compliant invoicing and billing tools and can manage custom EHR integrations
Why I like Helcim:
Helcim offers one of the strongest combinations of low-cost pricing and feature-rich billing tools among HIPAA-compliant processors. With no monthly fees and true interchange-plus rates, Helcim is attractive for healthcare providers that send recurring invoices, collect ACH payments, or need a cost-efficient virtual terminal.
Helcim’s willingness to sign a BAA gives healthcare practices the freedom to use its invoicing, recurring billing, and card-on-file features safely. And for clinics that process a large volume of card payments, its automated volume discounts can lower processing costs even further.
However, Helcim’s limited plug-and-play healthcare integrations and longer deposit times may be challenging for practices that rely heavily on EHR workflows. It’s best suited for providers who want advanced billing features at a low cost — but don’t need deep EHR integration out of the box.
- Monthly fee: $0
- Card-present fee: Interchange plus 0.15% + 6 cents to 0.4% + 8 cents
- Card-not-present fee: Interchange plus 0.15% + 15 cents to 0.50% + 25 cents
- American Express transactions: +0.10% + 10 cents
- Domestic ACH Transfers: 0.5% + 25 cents per transaction
- Hardware: $99 to $329
- Chargeback fee: $15 refundable
- Fully HIPAA-compliant with BAA
- Interchange-plus pricing, no monthly account fee
- Free traditional merchant account
- Automated volume discount
- Free access to virtual terminal, invoicing, and recurring billing management tools
- Secure card vault at no extra cost
- Accepts card and ACH payments
- Accepts HSA and FSA debit card payments
- Chargeback management and fraud prevention tools
- Online subscription with free customer portal
- Level 2 and 3 data optimization available for all merchant clients
- Free in-person and online surcharging program
Helcim is a great fit for cost-conscious healthcare practices that need strong invoicing and billing capabilities without monthly fees. However, clinics that rely on EHR-integrated payments or require faster deposits may prefer Square, Chase, or PaymentCloud.
Methodology: How I evaluated the best healthcare payment processors
I evaluated each payment processor using four main criteria, focusing on HIPAA compliance, affordability, and tools that support small healthcare practices:
- Pricing (20%): Assessed monthly fees, hardware costs, contract terms, and chargeback policies.
- Payment Features (30%): Reviewed support for HSA/FSA cards, ACH, invoicing, recurring billing, patient self-service tools, and whether the processor is fully HIPAA-compliant.
- Ease of Use (30%): Evaluated setup time, customer support hours, deposit speed, and availability of EHR and practice management integrations.
- Expert Score (20%): Considered transparency, value for money, scalability, and overall usability for healthcare providers.
Please note that my scores are based on the currently available features and information. This list will be regularly updated based on the latest technology and user demands to ensure that I provide you with the best information.
How to choose a healthcare payment solution
When choosing among healthcare payment processing companies, compliance should be the main priority. You should also look for providers that offer the most value for money in terms of payment features and fees.
- HIPAA compliance: Without a doubt, a prerequisite and a deal-breaker for any merchant processor that aims to provide a healthcare merchant account with additional management features.
- Security: Avoid merchant processors that do not have PCI Level 1 security. Additionally, choose a healthcare payment solution that offers advanced fraud protection and detection tools to effectively prevent chargebacks.
- Integrations: Ideally, you will want to have a merchant processor that’s compatible with most popular EHR systems, including what you currently use. Apart from EHR systems, you should also consider integration capabilities with other business software such as ecommerce, accounting, and appointment management.
- Credit card processing fees: In general, you will want to choose a merchant processor that offers transparent pricing. As much as possible, opt for solutions that offer interchange-plus pricing and low (or free) monthly fees. Look out for incidental costs such as chargebacks and surcharges for using additional payment functionalities like invoicing, virtual terminals, and payment gateways.
Looking for something different? Read our 10 best merchant services recommendations.
Frequently asked questions (FAQs)
A healthcare merchant account provides merchant services that are unique to healthcare service providers, such as hospitals and private practices. Most of the time, merchant processors that offer these services also come with HIPAA compliance, particularly if they provide additional functions such as scheduling, invoicing, and ecommerce.
Medical clinics can use non-HIPAA-compliant payment processors for simple credit card payment processing. However, this means that there is no integration with your practice management system and EHRs, which can cost you extra time and resources to keep track of your finances.
The telehealth business model is largely considered high-risk by merchant acquirers. This means a telehealth service will likely need a payment processor that supports high-risk merchant accounts in order to start accepting card payments. PaymentCloud is our top recommendation, especially if you also need a built-in invoicing feature, which will require HIPAA compliance from your payment processor.
No. PayPal, Stripe, and peer-to-peer payment processors like Zelle and Venmo are not HIPAA-compliant. These payment processors do not go into business associate agreements (BAAs) and also use client information for marketing purposes.
Bottom line
Healthcare practices need payment processors that protect patient information, support HIPAA-compliant workflows, and make it easy for patients to pay. While pricing matters, choosing a secure, compliant system is essential.
Square delivers the best overall value for most small and new healthcare practices, offering full HIPAA compliance, no monthly fees, strong payment tools, and useful EHR integrations. Practices with specialized needs, such as telehealth or high-risk services, may prefer PaymentCloud or Chase, but Square is the most accessible starting point for most providers.
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