Top 8 Payment Processing Tools for Healthcare Clinics [2025]

Clinic payments are more than simply swiping cards or issuing bills. When done correctly, payment processing maintains a steady cash flow, reduces administrative tasks, and keeps the checkout process easy for patients.

The issue? Determining which tools actually get those results without bringing on additional costs or workload to your already packed day.

That is why we have created this guide. We will review the top medical payment processing systems of 2025, including their capabilities, fees, and ideal applications. No frills, just the information you require.

Here's a brief overview of what we're going over:

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Top 8 Medical Payment Processing Platforms

Every clinic has different needs, ranging from solo mobile practitioners who require on-the-go payments to larger clinics that rely on insurance integrations. 

That’s why we’ve narrowed it down to eight platforms worth your attention in 2025. Each one is designed with healthcare in mind, and we’ll walk through what they offer, where they fit best, and their associated costs.

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1. Noterro - Best for Solo Practitioners & Small Clinics
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Noterro is built specifically for solo practitioners and small clinics that require both clinic administration and payment processing in one software.

You can accept payments, bills, and schedule appointments without having to switch systems. Whether you process credit cards, manage insurance claims, or collect deposits, it's all in sync. This saves you time and eliminates those administrative headaches we all know too well.

Features:

• Tailored Intake Forms: Customize intake forms to gather the exact information you need from patients, ensuring a smoother onboarding process.

• Flexible Appointment Reminders: Choose SMS, email, or phone reminders based on patient preference, reducing no-shows.

• Noterro GO: Designed for mobile practitioners, offering geo-booking, location-based scheduling, and the ability to manage your appointments while on the move.

• HIPAA/PIPEDA Compliance: Your payment processing and patient data management comply with stringent regulatory requirements.

• Insurance Billing Integration: Connect directly with insurers (TELUS and Availity) to simplify claims and track payments.

• AI-powered Charting: Voice-to-text notes, form summaries, and predictive tag suggestions for accurate note-taking and invoicing.

Capterra Rating: 4.8/5

Pricing: Starts from $28.05/month

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2. PaymentCloud - Best for High-Risk or Speciality Practices
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PaymentCloud specializes in serving high-risk or specialty practices, making it a solid choice for clinics dealing with unique payment processing needs. Whether you're handling large transactions or operating in a niche healthcare field, PaymentCloud provides reliable, secure payment solutions tailored to your needs. 

With features that simplify credit card payments, subscription billing, and fraud protection, it ensures that your practice can stay efficient while maintaining compliance with industry standards.

Features:

• Credit Card Processing: Accept all major credit cards, with flexible pricing based on transaction volume and risk level.

• Recurring Billing: Set up subscription or recurring billing for long-term treatment plans, memberships, or packages.

• Fraud Protection: PaymentCloud offers built-in fraud prevention tools to reduce chargebacks and protect both your practice and your patients.

• Custom Payment Solutions: Tailored to high-risk businesses, offering customizable solutions for different types of healthcare practices.

• Secure Payment Gateway: PCI-compliant payment gateway to ensure that patient payment data remains secure and encrypted.

• Mobile Payments: Process payments on the go, whether you're working remotely or in the clinic, with mobile-friendly features.

Capterra Rating: 4.7/5

Pricing: Custom pricing

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Here’s something for chiropractors: Best Chiropractic Software: Top 10 Tools for Your Practice

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3. InstaMed - Best for Insurance Payments

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InstaMed simplifies payment processing by concentrating on what most clinics find most difficult: insurance billing and patient payments. It's designed to make the claims process more efficient, lower admin workloads, and enhance cash flow by linking directly with insurance payers. 

InstaMed also provides patient payment solutions, so you can make payments quicker and more accurately.

Features:

• Insurance Billing Integration: Submit claims, verify eligibility, and track payment status all in one platform. This really simplifies the entire insurance process.

• Patient Payments: Patients pay online, over the phone, or through a secure patient portal. More choices mean you get paid sooner.

• Automated Payment Posting: Payments post electronically to your system, which reduces manual entry and mistakes.

• HIPAA-Compliant: Patient information and payment details remain safe and HIPAA-compliant.

• Real-Time Payment Tracking: Enjoy real-time visibility into payment statuses and claim resolutions. You'll receive a timely notification of when to expect payment.

Capterra Rating: NA

Pricing: Custom pricing

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Also read: Top 8 Medical Billing Software to Simplify Your Practice in 2025

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4. Podium - Best for Patient Communication & Payments

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Podium is an adaptable solution that integrates payment processing with patient communication software, making it an excellent option for those who need to automate both.

Built to enhance patient interaction, Podium enables you to send payment reminders, requests, and updates all via text, email, or chat. This multi-mode system streamlines the payment process while allowing for enhanced patient relationships.

Features:

• Text Message Payments: Send secure payment links over SMS so that patients can pay in seconds from their phone.

• Payment Reminders: Automate payment reminders, lowering late fees and enhancing cash flow.

• Patient Communication: In addition to payments, Podium facilitates SMS, email, and live chat for appointment reminders, reviews, and other patient communication.

• Secure Payment Gateway: Payments are processed securely through Podium's gateway, keeping patient information safe.

• Customizable Forms: Design customizable forms for billing information or patient intake, ensuring onboarding and bill payments become effortless. 

• Multi-location Support: Perfect for multi-location clinics, it ensures payments and communication are managed consistently across all locations.

Capterra Rating: 4.3/5

Pricing: Custom pricing

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5. Jane App - Best for Allied Health Practices

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Jane App is an all-in-one practice management platform that consolidates payment processing with scheduling and documentation. Ideal for allied health practices such as physiotherapists, massage therapists, and chiropractors, Jane App simplifies accepting payments, issuing invoices, and monitoring insurance claims in one place.

Features:

• Integrated Payments: Take credit card payments within the platform itself, with smooth transactions for your clinic.

• Insurance Billing: Streamline billing by connecting with insurance carriers, limiting back-and-forth, and accelerating payment cycles.

• Automated Payment Reminders: Send reminders through email and SMS to patients about future payments, with timely collection.

• Patient Payment Portal: Enable patients to review and pay their bills online using a secure, easy-to-use portal.

• Multi-location Support: Perfect for multi-location practices, Jane App ensures your payments are processed across all locations in a uniform manner.

Capterra Rating: 4.7/5

Pricing: Starts from $54/month

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Bonus read: Top 9 JaneApp Alternatives for Practice Management in 2025

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6. Chase - Best for Reliable Card Processing

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Chase has a solid payment processing option for clinics that want ease and dependability. If you've worked with Chase, you're aware of how reliable they are. Their system processes patient credit card payments easily, in the office or online.

With mobile payment capabilities and easy integration with clinic management, Chase provides an easy way to process payments while keeping your clinic and patient data safe.

Features:

• Credit Card Processing: Take all leading credit cards with the simple platform, both online and in-person.

• Mobile Payment Options: Accept payments anywhere with Chase's mobile solution. Perfect for site visits or when out and about.

• Integrated Payment Gateway: Link directly to your clinic's management system for seamless payment processing. No third-party software required.

• Security and Fraud Protection: Advanced security options, such as tokenization and encryption, safeguard patient payment information.

• Fast Setup: Begin to accept payments fast with low setup time.

Capterra Rating: NA

Pricing: Custom pricing

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7.  Stax - Best for Flat-Rate Subscription Models

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Stax provides a simple, flat-fee payment processing solution that's perfect for clinics that want to streamline their billing process.

With no surprises and a commitment to transparency, Stax helps simplify your monthly expenses while still offering strong features for payment acceptance and processing. It's especially helpful for clinics with high transaction volumes or clinics seeking a transparent, cost-effective solution.

Features:

• Flat-Rate Pricing: Have clear pricing with no per-transaction fees, allowing you to budget more easily for payment processing fees.

• Recurring Billing: Establish and manage subscription billing for regular patient treatment plans or membership.

• Advanced Reporting: Have in-depth reporting on your payments, fees, and transactions, so you can stay on top of your finances.

• Customizable Payment Pages: Design customizable payment pages for your clinic, where patients can pay directly on your website.

• Secure Payment Gateway: A PCI-compliant gateway secures your clinic's payment transactions and protects them from fraud.

Capterra Rating: 4.8/5

Pricing: Starts from $99/month

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8. Helcium - Best for Seamless Payment Integration

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Helcium is a payment processing platform that focuses on offering clear, transparent pricing with no hidden fees. 

Ideal for clinics that want straightforward billing and payment collection without surprises, Helcium makes managing patient payments and invoices simple and efficient. With features that support both in-clinic and mobile payments, Helcium ensures that your practice can accept payments securely, regardless of your location.

‍Features:

• Credit Card & ACH Payments: Accept payments via credit card or ACH transfers, giving patients more flexible ways to pay.

• Recurring Billing: Set up recurring billing options for patients with ongoing treatment plans or memberships, ensuring consistent payments.

• Integrated Invoicing: Manage invoices and payments directly within the platform, streamlining your financial workflows.

• Mobile Payment Solutions: Accept payments on the go, ideal for mobile practitioners or those who work in multiple locations.

• Security & Compliance: Helcium is PCI-compliant, ensuring that all patient payment data is securely handled and protected.
  
  

Capterra Rating: 4.5/5

Pricing: Charges per transaction

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How to Choose Medical Payment Processing Software

When selecting a medical payment processor, center on the features that have a direct influence on your clinic's bottom line and efficiency. The ideal platform should make payments easier, minimize admin time, and provide quick, safe transactions. These are the important features to consider:

1. Flexible Payment Options for Patients

Select a platform that supports a range of payment options, such as credit/debit cards, ACH transfers, and mobile payments. The greater the number of options you offer, the more convenient it is for patients to pay on time.

2. Mobile-Friendly Payments

Ensure that the payment processor you choose is mobile-friendly. This is important for mobile practitioners who want to accept payments while they are on the move.

3. Security and Compliance

Make sure the platform is HIPAA and PCI-compliant in order to secure patient data. Features such as encryption and safe payment gateways are a must in order to secure your clinic and patients.

4. Insurance Billing Integration

For clinics processing insurance claims, choose a processor that has direct integration with insurance systems. This minimizes manual entry of data and accelerates processing of claims.

5. Reporting and Analytics

An effective platform must provide reporting tools to monitor payments, late payments, and patient trends. You use this information to make informed decisions for your clinic.

6. Role-Based Access and Security Controls

Make sure the platform enables you to establish user permissions. This enables you to manage who has access to sensitive payment and patient information, keeping all data safe.

7. Transparent Pricing

Select a processor with transparent, easy-to-understand pricing. Steer clear of hidden charges or complex pricing structures that may result in additional unexpected expenses.

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Conclusion

Selecting the right payment processing software is essential for running a smooth, efficient clinic. The ideal solution will save you time, reduce errors, and help you get paid faster. 

Whether you're looking for flexible payment options, mobile-friendly solutions, or integrated insurance billing, the features that matter most are the ones that directly streamline your workflow and improve patient experience. 

Take the time to choose a platform that fits your clinic’s needs, and you'll see the difference in both your bottom line and the time you spend on admin tasks.

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