Top Healthcare Accounting Software Comparison: Features, Pricing & Benefits

Best Healthcare Accounting Software: TallyPrime, Xero, FreshBooks, Vyapar, and myBillBook are great for clinics, pharmacies, and laboratories, while AdvancedMD and Cliniko bring more end-to-end features for larger healthcare setups.

The global healthcare market will reach about USD 67.54 billion in 2025. This 14% growth from the previous year clearly tells how the healthcare industry is booming. As it will grow up to USD 111.65 billion till 2029, the responsibility of handling every task increases, be it patient management, diagnosis accuracy, or accounting operations. In healthcare, patient care and operational efficiency both are equally important.

Let’s come to accounting. A small mistake in accounting can delay reimbursements or even affect your cash flow. This is why many clinics, hospitals, and medical practitioners are now switching to healthcare accounting software to automate billing and track expenses.

Thus, we have listed 8 healthcare accounting Software that can help you save time and keep up with accuracy.

Comparison of Top Healthcare Accounting Tools in 2025

Find the best software for your healthcare business with this quick comparison.

List of Top Healthcare Accounting Software

Below-mentioned all the healthcare accounting software will ease managing payments, expenses, and financial data.

1. Tally Prime

TallyPrime is a great pick from the list of Medical accounting software in terms of features. Those who want smooth billing and complete GST compliance can go for it. If you have a clinic, lab, pharmacy, or hospital, you can generate accurate invoices, automate tax filing, manage payroll, and track inventory with very little manual intervention.

TallyPrime

4.4

Starting Price

₹ 750.00 excl. GST

Learn More

Key features of Tally Prime

• Accurate billing and tax management
• In-built intelligence for GST invoices
• Auto-filled GSTR-3B & GSTR-1 filing
• Accurate GST reconciliation (2A/2B)
• Tracks GST return activities
• Annual tax computation & ITC summary
• Automated payroll management
• Real-time inventory tracking for medical supplies
• Multi-level security with access controls
• Offline access to reports anytime

Tally Prime Pricing and Plans:

2. AdvancedMD

AdvancedMD is designed for healthcare providers who want end-to-end control over patient billing, insurance claims, and accounting. It helps you reduce claim denials, boost revenue, and automate the entire reimbursement process, from charge capture to A/R follow-ups.

With built-in analytics and a cloud-hosted model, you get a 360-degree financial health view of your practice anytime, anywhere.

AdvancedMD

4.9

Starting Price

Price on Request

Learn More

Key features of AdvancedMD

• End-to-end claims management
• Integrated clearinghouse
• Online patient payments
• Business analytics & reporting
• A/R control center with denial tracking
• Built-in medical coding support
• Medical scheduling with billing integration
• Centralized billing for multi-locations
• Cloud-hosted secure medical billing
• Claim Inspector for error-free submissions
• ERA processing & e-remittance
• E-eligibility insurance verification
• EHR integration with auto data sync

AdvancedMD Pricing and Plans

Pricing is available on request. Contact the Techjockey team for pricing.

3. Cliniko

Cliniko is perfect for clinics and independent healthcare practitioners who want to simplify invoicing, payments, and financial reporting without getting into complicated accounting systems. It makes it easy for patients to pay online while helping you track revenue, taxes, refunds, and expenses, all from the same dashboard.

Clinion EDC

4.3

Starting Price

Price on Request

Learn More

Key features of Cliniko

• Create invoices directly from the appointment calendar
• Mobile-friendly online payments
• Multiple custom payment types
• Easy tax setup on products
• Split payments & third-party billing
• Track refunds and convert to credit
• Record expenses for tax reporting
• Financial reports for revenue & dues
• Xero accounting integration

Cliniko Pricing and Plans:

4. Alignbooks

AlignBooks is a good choice for healthcare facilities that want to automate everyday accounting tasks like billing, invoicing, document management, and workflows. You can customize invoices, automate reminders, attach supporting documents, and manage GST + payroll from a single system.

AlignBooks

3.8

Starting Price

₹ 10000.00 excl. GST

Learn More

Key features of Alignbooks

• Automated workflows for billing & invoicing
• Service item billing with tax tracking
• Custom invoice templates with logo & GST info
• Complete GST & payroll management
• Easy document management with scanned attachments
• Workflow automation from quote to payment

Alignbooks Pricing and Plans:

There are four plans available – Basic, Premium, Ultima, and AlignBooks Plus. You can contact the Techjockey team for pricing.

5. Xero

Xero is ideal for healthcare clinics, diagnostic centers, pharmacies, and small hospitals that want to shift from manual paperwork to a clean, paperless accounting system.

You can automate invoicing, track expenses, and reconcile bank transactions in one place. Xero also gives real-time financial insights to help you understand your cash flow, profitability, and business growth.

Xero Accounting Software

3.9

Starting Price

$ 29.00      

Learn More

Key features of Xero

• Paperless financial record-keeping
• Automations for invoicing & expense management
• Trend analysis & real-time financial insights
• Automatic bank reconciliations
• GST/tax-friendly accounting reports
• Bank feed for daily transaction imports
• Cash flow tracking in real time
• Online employee collaboration via the Xero Me app

Xero Pricing and Plans:

6. FreshBooks

FreshBooks works well for healthcare professionals who want stress-free invoicing and easy expense tracking.

Whether you’re managing patient payments, consultation billing, or reimbursements, FreshBooks lets you create invoices in minutes, scan receipts from your phone, and collaborate with your accountant without back-and-forth emails.

Freshbooks

3.9

Starting Price

$ 2.10      

Learn More

Key features of FreshBooks

• Fast professional invoicing with automated taxes
• Mobile receipt scanning & expense tracking
• Customizable chart of accounts
• Accountant access for real-time collaboration
• 100+ integrations for automated workflows
• Embedded payroll and bank reconciliation

FreshBooks Pricing and Plans:

7. Vyapar

Vyapar is a great fit for Indian healthcare businesses like pharmacies, clinics, labs, and distributors that need strong GST billing with complete accounting accuracy. Its double-entry accounting system helps keep your books balanced without manual calculations.

Vyapar Billing Software

4.5

Starting Price

₹ 1099.00 excl. GST

Learn More

Key features of Vyapar

• Double-entry accounting with automatic balancing
• Accurate journal entries & ledger management
• Real-time Profit & Loss reports
• Expense tracking with categorization
• GST-compatible invoicing and auto tax calculations
• Auto-generated GSTR reports
• Cash flow dashboard for receivables & payables
• Payment tracking for UPI, cash & bank transfers
• Alerts for pending payments
• 100% data security & cloud backup
• Works online & offline

Vyapar Pricing and Plans:

8. myBillBook

myBillBook helps healthcare businesses generate fast, GST-compliant invoices while keeping track of revenue, expenses, and profitability. Whether you run a clinic, pharmacy, lab, or medical supply store, you can customize bills, automate reports, and share invoices through WhatsApp or email, making payment collection faster and more convenient.

myBillBook

4.5

Starting Price

₹ 3599.00 excl. GST

Learn More

Key features of myBillBook

• GST-compliant invoices with HSN/SAC codes
• Custom invoice templates with bilingual formats
• Profit & Loss, sales summaries & performance dashboards
• Accrual and cash accounting support
• Financial reports, including balance sheet & cash flow
• Tracks receivables, reimbursements & medical payments

myBillBook Pricing and Plans:

Conclusion

If you’re running a healthcare business, accounting doesn’t have to be complicated anymore. With the right healthcare accounting software, you can automate billing, reduce claim delays, manage GST or taxes, track expenses, and get clear insights into your cash flow, all without depending on manual spreadsheets.

Choose the one that fits your size, budget, and workflow, and spend more time focusing on patient care instead of paperwork.