Summary: “Epic, Oracle Health, Athenahealth, NextGen Healthcare, and AdvancedMD lead our list of the best pulmonology EMR systems, with strong support for PFT tracking, sleep study workflows, and CPAP compliance. Veradigm, eClinicalWorks, Hero EMR, Healthray, and Tebra are also strong options reviewed in this guide. At Transcure, we integrate with all these EMR systems, so switching your billing partner doesn’t mean switching your system.”
Pulmonologists still log real after-hours time in the EHR, roughly 20 minutes past 7 pm and nearly 38 minutes outside scheduled hours, according to a study presented at the American Thoracic Society’s 2025 conference.
That’s notable given pulmonology’s procedure-heavy schedule, which often requires providers to manage multiple visits and procedures in the same day.
Much of that burden traces back to PFT results, sleep study data, and CPAP compliance numbers that often land in the chart as a scanned PDF instead of structured, trendable data. This forces pulmonologists to re-enter numbers a machine already recorded.
Here are the 10 best EMR systems for pulmonology practices. These include major platforms like Epic and Oracle Health and specialty-built tools like Hero EMR and Healthray, ranked by how well each handles PFT integration, sleep workflows, and pulmonology billing.
| Pulmonology EMRs | Rating | Core Strengths |
|---|---|---|
Epic
|
Strengths: Deep clinical workflows, strong interoperability, large health-system support | |
Oracle Health
|
Strengths: Enterprise-scale care, hospital connectivity, unified patient records | |
Athenahealth
|
Strengths: Cloud-based EHR, integrated billing, scheduling, and RCM | |
AdvancedMD
|
Strengths: Pulmonology templates, integrated billing, scheduling, patient tracking, and telehealth | |
NextGen Healthcare
|
Strengths: 500+ pulmonary and sleep-specific enhancements, PFT and sleep workflows, DME ordering, real-time patient scorecards | |
Veradigm
|
Strengths: Ambulatory care, EHR and practice management, clinical data exchange | |
eClinicalWorks
|
Strengths: All-in-one EHR and PM, patient portal, telehealth, and interoperability | |
Hero EMR
|
Strengths: Specialty-focused charting, customizable workflows, streamlined practice operations | |
Greenway Health
|
Strengths: Cloud-based EHR, practice management, patient engagement, and RCM | |
Tebra
|
Strengths: Independent practice management, scheduling, billing, and patient engagement |
Epic is one of the most widely used enterprise EHR platforms, with workflows designed for more than 60 specialties. For pulmonology, its tools can support specialty documentation, procedures, scheduling, referrals, and coordination across different care settings.
It also offers support for pulmonology procedures through its Lumens endoscopy application, which can handle scheduling, procedure documentation, results, images, and follow-up.
For larger pulmonary groups and health systems, Epic’s biggest advantage is how much clinical information can stay connected within one patient record. Its integrated scheduling can also handle specialty visits, procedures, and diagnostics.
Key Features
- MyChart: Gives patients access to appointments, test results, medications, and messages.
- Lumens: Supports procedure scheduling, documentation, images, results, and follow-up.
- Care Everywhere: Allows providers to exchange patient information across participating healthcare organizations.
- Epic Hyperspace: Provides the main workspace for accessing clinical and patient information.
2. Oracle Health
Oracle Health is an enterprise EHR designed to connect clinical information across different departments and care settings. Its current platform includes personalized workflows, patient timelines, clinical decision support, and AI-powered tools.
This EHR also specifically lists pulmonology among the specialties supported by its Clinical AI Agent.
For pulmonologists, the platform’s focus on connected patient information can be useful when care involves multiple providers, departments, or facilities. Oracle Health also offers integrated claims, prior authorization, and payment workflows.
Key Features
- Oracle Health EHR: Centralizes patient records, clinical documentation, and care workflows.
- Oracle Health Clinical AI Agent: Assists with clinical documentation and specialty workflows.
- Oracle Health Patient Portal: Lets patients access health information and interact with their care team.
- Oracle Health Clinical Decision Support: Provides relevant information to help clinicians during care.
3. Athenahealth
athenahealth is a cloud-based EHR and practice management platform designed for ambulatory practices. Its athenaOne platform combines clinical documentation, practice management, patient engagement, and revenue cycle tools in one system.
For pulmonology practices, this can help keep clinical and administrative workflows connected instead of relying on separate systems.
The platform also emphasizes interoperability, allowing providers to exchange health information with other organizations. Its revenue cycle tools support claims management, eligibility checks, payment posting, and denial follow-up.
Key Features
- athenaOne: Combines EHR, practice management, patient engagement, and billing tools.
- athenaClinicals: Handles electronic clinical documentation and patient records.
- athenaCollector: Supports claims, payment posting, and revenue cycle management.
- athenaCommunicator: Provides patient messaging and appointment communication.
4. AdvancedMD
AdvancedMD combines EHR, practice management, and medical billing tools in a cloud-based platform.
Its EHR includes specialty-specific templates and customizable workflows, while its practice management tools cover scheduling, patient registration, insurance verification, and other day-to-day administrative tasks.
Its billing capabilities are another major part of the platform. AdvancedMD, as a popular EHR, provides tools for claims management, payment processing, patient statements, and revenue cycle management.
Key Features
- AdvancedEHR: Provides electronic charting, clinical documentation, and customizable templates.
- AdvancedPM: Handles scheduling, registration, insurance verification, and practice operations.
- AdvancedRCM: Supports claims, payments, denials, and revenue cycle workflows.
- Telemedicine: Supports virtual visits directly through the platform.
5. NextGen Healthcare
NextGen Healthcare stands out for its dedicated pulmonary and sleep medicine tools. The platform offers more than 500 specialty-specific enhancements, including templates for PFT findings, spirometry, six-minute walk tests, bronchoscopy, thoracentesis, and sleep testing.
It also supports DME and sleep-test ordering, making it particularly relevant for practices that manage both pulmonary and sleep patients.
Practices can use its EHR, scheduling, claims, analytics, and AI documentation tools within the broader platform. This makes NextGen an option for practices that want pulmonary-specific functionality without separating their clinical and administrative systems.
Key Features
- PFT & Spirometry Templates: Supports documentation for PFT findings, spirometry, and six-minute walk results.
- Sleep Test Ordering: Streamlines ordering for polysomnograms, MSLT, MWT, and other sleep tests.
- ScoreCard: Displays data such as spirometry, pulse oximetry, and sleep-related scores over time.
- NextGen Clinical AI: Converts patient-provider conversations into structured SOAP notes.
6. Veradigm
Veradigm EHR is an ambulatory platform built around customizable workflows and specialty-specific content. Its tools include one-click templates, smart lists, automated reporting, and an ambient scribe that can turn conversations into structured clinical notes.
The platform also supports telehealth and mobile access, which can help physicians manage clinical work beyond the traditional office workstation.
For practices focused on the financial side of operations, Veradigm also offers integrated revenue cycle services covering payer communication, coding, claims, and denial management.
Key Features
- One-Click Templates: Quickly populate patient information from previous visits or conditions.
- Smart Lists: Surfaces commonly ordered items based on diagnoses and ordering patterns.
- Veradigm Ambient Scribe: Converts visit conversations into structured clinical notes.
- Veradigm EHR Mobile: Lets physicians review schedules, messages, and other patient information on the go.
7. eClinicalWorks
eClinicalWorks is a cloud-based EHR and practice management platform that can support the clinical and administrative needs of a pulmonology practice. It combines clinical documentation, scheduling, patient engagement, telehealth, and revenue cycle management in one system.
For pulmonologists, the platform also offers tools that can reduce repetitive documentation and administrative work.
Its AI features can assist with clinical notes and patient information. The Healow suite supports patient appointments, health information, communication, and virtual care. On the billing side, eCW provides tools for eligibility checks, claims, payments, and RCM.
Key Features
- AI Assistant: Helps pulmonologists with clinical documentation, patient records, and routine charting tasks.
- healow: Gives pulmonary patients access to appointments, health information, messages, and other digital services.
- healow Genie: Handles common patient requests through voice, text, email, and chatbot interactions.
- EHR Templates: Helps pulmonologists document visits and organize pulmonary patient information.
8. Hero EMR
Hero EMR is a modern electronic medical record platform built to simplify clinical documentation and practice workflows. Its interface is designed to make everyday charting and patient management easier for providers.
For pulmonology practices, the main value comes down to how well the platform fits existing workflows.
Practices can review its documentation tools, templates, and integrations based on their specific needs. This is especially important for pulmonary practices that manage diagnostic testing, referrals, and recurring follow-up visits.
Key Features
- Electronic Medical Records: Keeps patient charts and clinical information in one place.
- Clinical Documentation: Helps providers create and manage patient notes.
- Customizable Workflows: Allows practices to adapt workflows to their needs.
- Patient Management: Organizes patient information and related activities.
9. Greenway Health
Greenway Health offers cloud-based EHR and practice management tools that can support the daily needs of a pulmonology practice.
Its Intergy platform combines clinical documentation, scheduling, patient communication, and practice management. This gives pulmonary teams one place to manage patient records and routine office workflows.
Greenway also puts a strong focus on the financial side of practice operations. For pulmonology practices, this can help connect clinical work with the billing process. The system also provides reporting tools that can help practices monitor financial and operational performance.
Key Features
- Intergy EHR: Manages pulmonary patient records, clinical documentation, and office workflows.
- Intergy Practice Management: Supports scheduling, registration, insurance verification, and daily practice operations.
- Greenway Revenue Services: Supports claims, payments, and revenue cycle activities.
- Patient Portal: Lets pulmonary patients access health information, communicate, and manage appointments.
10. Tebra
Tebra combines EHR, practice management, patient engagement, and billing tools in one cloud-based platform.
For a pulmonology practice, this can simplify routine tasks such as charting, scheduling, patient communication, and payment collection. Its EHR also provides customizable templates that can be adapted to a practice’s documentation needs.
Tebra also connects clinical workflows with billing and revenue cycle management. Its platform can handle eligibility, claims, payment posting, patient statements, and collections. This can help pulmonary practices keep more of their administrative workflow in one system.
Key Features
- Tebra EHR: Supports pulmonary documentation, patient records, and customizable clinical workflows.
- Tebra Practice Management: Handles scheduling, registration, insurance, and day-to-day practice operations.
- Tebra Billing: Supports claims, payment posting, patient balances, and billing workflows.
- Patient Portal: Gives pulmonary patients access to appointments, messages, forms, and health information.
How We Picked the Best Pulmonology EMR Software?
We reviewed each EMR based on the features that matter most to a pulmonology practice. Our review looked at clinical documentation, pulmonary testing workflows, sleep medicine capabilities, scheduling, patient management, and integrations.
Moreover, we researched information from the EMR vendors’ official websites, product pages, feature documentation, and available platform resources. When a vendor offered pulmonary or sleep-specific features, we looked at those features more closely. We also considered if the platform supports tools like PFT documentation, sleep study workflows, and clinical reporting.
Finally, we compared how each system connects clinical work with practice management and billing. We looked at features such as claims management, eligibility, payment workflows, revenue cycle tools, and reporting.
Does Transcure Provide Support for Major Pulmonology EMR Software?
Transcure provides pulmonology billing services that can work with the EMR and practice management system your practice already uses. Our team can support practices using platforms such as Epic, Oracle Health, athenahealth, NextGen, eClinicalWorks, and other EMR systems.
At Transcure, we handle CPT, ICD-10, and HCPCS coding, including pulmonology codes such as 94060, 94618, 71271, 99291, and 99292. We work around your existing clinical workflow instead of asking your practice to change its EMR.
We have processed more than 2.7 million claims and report a first-pass clean claim rate of up to 99%, along with an average A/R of about 24 days. These processes help keep claims moving and give your team more time to focus on patient care.
If you are considering a new pulmonology EMR, we can also help you understand how its billing workflow may affect your revenue cycle.
What To Look For in a Pulmonology EHR Software?
Choosing an EHR for a pulmonology practice involves more than basic charting and scheduling. Your practice needs an EHR that can handle pulmonary testing, procedure documentation, recurring follow-ups, and the data that comes with respiratory care.
Here are the key areas to evaluate before choosing a pulmonology EHR software:
Pulmonary Testing and PFT Integration
Pulmonology practices rely heavily on pulmonary function testing, including spirometry and other PFT measurements. Your EHR should make it easy to document these results and review them alongside the patient’s clinical history.
Look for PFT integration that can bring test results into the patient’s chart without requiring your team to manually enter every value. Trend views are also useful when you need to compare results across multiple visits.
Sleep Medicine and CPAP Workflows
If your pulmonology practice also manages sleep-related conditions, check how the EHR handles sleep studies and CPAP-related information. The system should support documentation for sleep testing, follow-up visits, and ongoing patient monitoring.
You should also check whether the EHR can connect with sleep testing systems or other relevant devices. This can reduce duplicate data entry and make long-term follow-up easier.
Customizable Clinical Templates
Pulmonary visits can vary significantly. A new patient evaluation may require different documentation from a COPD follow-up, asthma visit, PFT review, or post-procedure appointment.
Customizable templates allow your team to create workflows around these different visit types. Look for templates that can be adjusted without making everyday charting more complicated.
Interoperability and Diagnostic Data
Pulmonary care often involves information from different sources, including imaging, laboratory results, PFT systems, sleep studies, referrals, and hospital records. An EHR should make this information easy to access within the patient’s chart.
Check which interoperability standards and integrations the platform supports. Also look at how easily your practice can exchange records with hospitals, referring providers, diagnostic systems, and other connected organizations.
Reporting and Data Tracking
A useful pulmonology EHR should make clinical and operational information easy to review. Reporting tools can help practices monitor patient populations, testing results, appointments, documentation, and financial performance.
For pulmonary practices, also consider if the system can track relevant testing and clinical measures over time. The ability to turn stored data into useful reports can be valuable for both patient care and practice management.
Frequently Asked Questions
Does Pulmonology EMR Software Support Sleep Medicine Workflows?
Some pulmonology EMRs include sleep medicine features such as sleep study ordering, documentation, and patient monitoring. If your practice provides sleep-related care, review these capabilities during an EHR demo and confirm they match your clinical and administrative workflow.
Can Transcure Work With Your Pulmonology EMR?
Transcure works inside 43+ EHR platforms, including Epic, athenahealth, eClinicalWorks, AdvancedMD, and NextGen. Our billing team works with your existing system instead of requiring an EMR migration. Support includes coding, claims, payment posting, denial follow-up, and A/R management.
How Much Does Pulmonology EHR Software Cost?
Pulmonology EHR costs vary based on the vendor, number of providers, features, implementation, and billing options. Some systems charge monthly per provider, while others use customized pricing. Ask about setup fees, training, integrations, support, and additional costs before signing.
What Are the Benefits of Using a Pulmonology-Specific EHR?
A pulmonology-specific EHR can provide workflows designed around pulmonary testing, procedures, sleep studies, and recurring respiratory care. It can also reduce manual documentation, organize clinical data, and connect patient records with scheduling, billing, and reporting.
Does Changing an EMR Improve Medical Billing?
Changing an EHR may improve billing when the current system lacks important features or creates workflow problems. However, an EHR change is not always necessary. Working with experienced pulmonology billing companies can help improve coding, claims, denials, and A/R while allowing your practice to keep its current EMR.
