EHR Comparison

athenahealth vs eClinicalWorks for Doctors 2024: Full Comparison

athenahealth and eClinicalWorks are two of the most widely used outpatient EHR platforms, but they serve practices with very different financial profiles and workflow preferences. We compared both on billing performance, clinical documentation, and value-based care tools.

By MedTech Review EditorialUpdated: July 20, 20249 min read✓ Medically Verified

athenahealth and eClinicalWorks together serve over 250,000 U.S. physicians, but they target different practice needs. athenahealth's percentage-of-collections pricing model aligns incentives with revenue performance, while eClinicalWorks' flat fee favors high-revenue practices. We compared both platforms on net collection rates, MIPS quality reporting quality, patient portal adoption, and implementation experience for outpatient practices of 3–15 providers.

Product Comparison

Product	Rating	Price	Best For
athenahealth EHR	★ 4.7	~8% of collections	Billing performance & VBC	View →
eClinicalWorks (eCW)	★ 4.4	From $449/mo per provider	High-volume flat-fee practices	View →
NextGen Healthcare	★ 4.3	From $299/mo per provider	Specialty group practices	View →
Greenway Health	★ 4.1	Custom pricing	Ambulatory multi-specialty groups	View →
Allscripts Professional	★ 4.0	From $200/mo per provider	Practices with legacy Allscripts installs	View →

Pros & Cons

✓ Pros

athenahealth's 97%+ first-pass claim rate is the highest independently verified rate among all outpatient EHR platforms
eClinicalWorks' flat monthly fee becomes significantly more affordable for practices billing over $600K/year per provider
athenahealth's Epocrates drug reference integration gives physicians point-of-care drug information within the EHR workflow
eClinicalWorks' healow app delivers one of the highest patient portal adoption rates among non-Epic EHR platforms

✗ Cons

athenahealth at 8% of collections costs $4,000–8,000/month for a typical internal medicine practice — significantly above flat-fee alternatives
eClinicalWorks paid a $155M DOJ settlement in 2017 for EHR certification misrepresentation — a decision factor for some practices
Neither platform offers the depth of specialty-specific clinical content that ModMed or Nextech provide for procedure-intensive specialties

Frequently Asked Questions

Is athenahealth worth the 8% fee compared to eClinicalWorks' flat rate?▾

For practices collecting under $500,000/year per provider, athenahealth's percentage-based fee (~$40,000/year) is comparable to or exceeds eClinicalWorks' flat fee ($5,400/year). For practices collecting $800,000+/year, athenahealth's fee grows to $64,000+/year — significantly more. However, athenahealth's net collection rate improvement of 3–5% over self-managed billing often offsets the fee difference.

How do athenahealth and eClinicalWorks compare on MIPS quality reporting?▾

athenahealth has the most automated MIPS reporting workflow — quality measures are calculated automatically from clinical documentation, and the platform submits directly to CMS via qualified registry. eClinicalWorks also supports MIPS reporting through its Population Health module, but requires more manual data reconciliation. athenahealth clients consistently achieve higher MIPS performance scores in national benchmarks.

Which platform is easier to implement — athenahealth or eClinicalWorks?▾

athenahealth is cloud-native with no server infrastructure requirements and a structured onboarding program averaging 8–12 weeks for 3–5 provider practices. eClinicalWorks can be deployed on-premise or cloud-hosted and typically takes 10–16 weeks for full implementation. Both require dedicated staff training time, but athenahealth's implementation support team is consistently rated higher in post-go-live satisfaction surveys.

Can I switch from eClinicalWorks to athenahealth and keep my patient data?▾

Patient demographic data, problem lists, medications, allergies, and immunizations can be migrated via CCDA export. Historical clinical notes and billing history typically require manual migration or third-party conversion services. Most practices plan a 90-day parallel billing period where both systems run simultaneously to ensure billing continuity. Budget $5,000–15,000 for a comprehensive data migration.

Our Top Pick

athenahealth — Best Outpatient EHR for Billing Performance

athenahealth's 97.6% first-pass claim rate and automated MIPS reporting make it the highest-performing outpatient EHR for practices that want billing results rather than just billing software.

Request a Free athenahealth Demo →

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