Top Challenges of Electronic Health Record (EHR) Implementation

What is an electronic health record and EHR system?

An electronic health record is a digital version of a patient’s medical chart. It includes the patient’s medical history, diagnoses, medications, treatment plans, immunization dates, allergies and other key details. EHRs improve on paper medical records by providing more accurate, up-to-date information and a complete, timestamped view of patient care.

Authorized users, like clinicians and front-office staff, access these records through an EHR system. These systems store and manage patient data for an entire practice, allowing information to be shared securely and efficiently with pharmacies, labs, specialists and medical imaging facilities.

EHRs are now standard across U.S. healthcare. According to the most recent National Electronic Health Records Survey (NEHRS), 88.2 percent of U.S. office-based physicians have adopted EHR systems. Similarly, the Office of the National Coordinator for Health Information Technology reports that nearly 96 percent of non-federal acute-care hospitals use certified EHR systems. This widespread adoption underscores how EHR technology enhances efficiency, streamlines communication, and ultimately improves patient outcomes.

How to overcome EHR implementation challenges

Medical practices typically encounter four primary challenges when implementing an EHR system. Here’s an overview of these challenges and tips on overcoming them.

Challenge 1: Budgeting and finding the right partner

There’s no getting around the fact that EHRs are expensive and time-consuming. Here are some tips for budgeting adequately and finding the right partner vendor to ease your implementation: 

• Budget with flexibility: EHR implementation costs can range anywhere from $15,000 to $70,000, depending on the size of your organization and the complexity of your system. Because unexpected costs are common, build in a buffer for additional resources or emergency support when planning your budget. A reliable vendor should help you estimate total costs, including setup, integration and ongoing support.
• Don’t chase the lowest bid: As with most technology investments, you often get what you pay for. The cheapest vendor may lack the expertise or staffing to keep your project on schedule, leading to delays and hidden costs later. Look beyond price to evaluate experience, reputation and scope of service.
• Choose a certified, experienced vendor: Select a partner with a proven track record and certification from the Office of the National Coordinator for Health Information Technology (ONC). The earlier you engage your vendor, the smoother your implementation will be. When evaluating candidates, create a detailed checklist of your needs and a clear project timeline to compare options fairly.

Challenge 2: Communication breakdowns and training

Training gaps and poor communication can derail an EHR rollout. A 2025 U.S. report by KLAS Research found that training remains one of the weakest links in EHR implementations. And a study in Frontiers in Medicine confirmed that insufficient training and technical support are major obstacles in system-wide deployments. These findings underline the need for clear user workflows, structured training programs and ongoing support.

Here are some tips to avoid communication breakdowns and ensure everyone can use the system confidently: 

• Identify all the variables in your EHR implementation: Start by mapping out everyone who plays a role in the rollout, including clinicians, administrative staff, IT teams and even patient representatives. A full stakeholder map helps you understand how each group will use the system and ensures their perspectives are factored into your training plan.
• Loop in your vendor’s team early: Include your EHR vendor’s staff in your training efforts so they understand how your practice actually works. When they’re familiar with your day-to-day workflows, they can better tailor the system to your needs. Keep their support team close at hand during launch and encourage employees to reach out and test every feature until they’re confident using it.
• Make sure everyone completes training: Every user should finish training before go-live — no exceptions. Consider a competency-based approach where staff demonstrate proficiency before getting full system access. For anyone who joins late or needs a refresher, have a clear backup plan for post-launch employee training.
• Designate an EHR project leader: Choose one person to serve as the point of contact between C-suite executives, tactical project leads, vendors and staff. This project leader keeps communication flowing and ensures that questions and issues don’t get lost between teams.
• Keep communication open at every level: Set up regular check-ins, create dedicated channels for troubleshooting and maintain a shared FAQ or quick-reference guide to address recurring issues. Open communication prevents confusion and helps your team feel supported during the transition.

Challenge 3: Contingency planning and leadership support

If there’s one constant with EHR launches, it’s that something will go wrong. According to the KLAS Research EHR implementation report cited above, about 40 percent of healthcare leaders said they experienced significant issues during their organization’s EHR implementation — and only 38 percent considered their rollouts fully successful. 

Here’s how to minimize disruption when the unexpected happens.

• Empower your launch team: Give your EHR launch staff the authority and resources to handle issues as they arise. A clear escalation plan helps resolve emergencies quickly and reduces frustration for both staff and patients. Set tiered support levels with defined response times; for instance, critical issues should be addressed within 15 minutes, while noncritical concerns can be resolved within a few hours.
• Plan ahead for problem resolution: Establish guidelines for identifying and fixing technical issues before go-live. Create an incident response playbook that outlines common problems and their solutions, and assign ownership for each category. Make sure your team documents fixes for recurring issues so solutions are easy to find next time.
• Secure visible leadership support: Strong leadership is essential during an EHR rollout. Executives should be active and visible, hosting town halls, joining rounding sessions, and communicating directly with staff. When leaders champion the system’s benefits and stay present during go-live, it reinforces confidence and helps teams adapt faster.

Challenge 4: Workflows

Workflows are a critical focus for healthcare professionals when planning, documenting and communicating information during an EHR rollout. According to the KLAS Research data (cited above), workflow design and system integration remain among the top challenges for healthcare organizations — and among the areas where leaders report the lowest satisfaction post-implementation.

Not all healthcare workflows are the same; some are more complex and directly tied to patient safety and well-being. Here are a few of the most sensitive areas to plan for carefully:

• Blood banks: Lives depend on precise tracking. It’s crucial to ensure your EHR includes real-time inventory monitoring, cross-matching verification protocols and automated alerts for critical supply levels.
• Medication reconciliation: Before go-live, confirm that your EHR can accurately track medications throughout a patient’s stay. It should automatically flag potential drug interactions, dosage discrepancies and allergy conflicts.
• Patient movement: Tracking where patients are within a facility is essential for continuity of care. Modern EHR systems should integrate with real-time location systems (RTLS) to provide accurate updates across departments.
• Level of care: Properly documenting a patient’s care level — whether they’re in the emergency room, ICU or step-down unit — is vital for both clinical accuracy and the medical billing process.
• Careful transport: Every patient transfer should be logged precisely. Your EHR should record transport requirements, equipment needs and staff assignments for each move.

Why EHR implementations are so complex

While EHR systems may look seamless and intuitive once they’re up and running, implementing one is a major project that demands time, resources and coordination. The timeline can vary widely; most implementations take six months to a year, but particularly large or complex systems can take 18 months to two years from planning to full adoption. Success depends not just on technical setup but also on user adoption, measurable cost savings and visible improvements in patient care.

Here are the main factors that make EHR implementation so complex:

• Clinicians and front-end staff must embrace the system: Getting every team member on board is essential. Practices must define exactly what their EHR needs to do, choose a platform that meets those needs and configure it to support clinical and administrative workflows. Then comes training, testing and refinement. A pilot phase helps uncover initial issues, but ongoing support and optimization are key to achieving full adoption.
• Technical specifications must be set, adjusted and monitored: IT teams play a central role in ensuring a smooth rollout. They must thoroughly test hardware, software and network interfaces before go-live, especially if telemedicine tools are involved. With many organizations now adopting cloud-based EHRs, maintaining sufficient internet speeds with robust business broadband — typically at least 25 Mbps for optimal performance — is critical. Backup and downtime procedures should also be established, and all users must have secure access credentials.

With so many variables at play, every practice should start by defining clear goals for success and creating contingency plans to address common implementation challenges.

Best EHR software

The best medical software improves patient-facing processes, streamlines workflows and supports administrative and back-end functions. Consider the following top EHR platforms to help you find the right option for your practice:

• DrChrono: DrChrono is a versatile EHR system with an average configuration time of 30 to 60 days. The company offers implementation and training services for all customers, regardless of plan tier, including a dedicated account manager to ensure the platform is tailored to each practice’s needs. Our DrChrono review explains how this vendor helps practices create templates to automate workflows and assists with enrollment and credentialing with app providers, labs, pharmacies and other third parties. 
• athenahealth: athenahealth reports an average implementation period of around 11 weeks, though installations for new practices with minimal data can take as little as a month. As our athenahealth review explains, every practice is assigned a Customer Success Manager (CSM), and EMR training and live support are included in the subscription cost. The platform also now features AI-powered documentation tools that can reduce clinical documentation time by up to 30 percent.
• Tebra (formerly Kareo): Implementation and training costs are included in all standard Tebra subscriptions. The setup process can take up to six weeks as Tebra configures an interface within the software to connect with pharmacies and Medicare and Medicaid insurers. Our Tebra review details how each account manager uses milestones to guide healthcare providers through setup and provides one-on-one staff training. Tebra has also introduced enhanced telehealth tools integrated directly into the EHR workflow.
• AdvancedMD: AdvancedMD provides a two-day on-site implementation service at no additional charge to practices with collections exceeding $200,000 per month. Other practices pay around $5,000 for full staff training and system configuration, which includes 20 hours of one-on-one sessions, online courses and help customizing templates, macros and workflows. Most systems go live within approximately 11 weeks. As our AdvancedMD review notes, each practice is paired with an account manager who remains available post-launch. Recent updates include improved interoperability features that enable seamless data exchange with more than 600 healthcare organizations.
• CareCloud: CareCloud offers three implementation options, ranging from full-service onboarding with its Enterprise plan to self-guided online setup with the Essentials tier. Its newest version includes predictive analytics tools that help practices identify at-risk patients and optimize scheduling efficiency. Prices vary based on practice size, specialty and support level. Our detailed CareCloud review explores these differences.