The implementation of a fresh Electronic Medical Records (EMR) Software, whether from paper charts or another already-in-use EHR and PM System, poses significant challenges and financial strains for a healthcare practice. This article discusses the common EHR System implementation challenges and costs along with strategies and solutions on how to tackle these challenges, to make the most out of your EMR Software.

Becoming eligible to the MIPS  is one of the top reasons practices go headfirst into EMR Software implementation. What they don’t realize is that a signed contract with a qualified EHR Software fulfills this requirement. Rushing into implementation causes major loss in productivity and efficiency and practices often are unable to survive that. To reap the benefits of EHR Software you need to give it appropriate time and consideration to minimize the cost and avoid uncertain circumstances.

EHR Software Implementation Costs


Whether you are implementing your first EMR & Practice Management Software or if you are transitioning it is important to understand that while discussing the total EHR implementation cost breakdown there are costs other than Financial Cost that cannot be overlooked. These are challenges faced during the transition. If these challenges are dealt with beforehand the transition becomes a lot easier, seamless and economical.

Inconvenience for Staff

For some employees, change in organizations can be pretty hard to digest. When the staff within an organization is not willing to accept a change, they try to resist it in multiple ways. In medical practice, this resistance to change might come from the support and clinical staff all the way up to the executive members, the board of directors, and the stakeholders.

It is essential that Electronic Health Records (EHR) Software is implemented in such a way that the resistance is minimized and properly catered to. There needs to be a culture of positivity and acceptance for the change throughout the entire practice. The staff needs to be on the same page on the fact that this change will bring about better workflow and increase job satisfaction.

Productivity Loss


With the implementation of a new EMR Software System, the productivity of the staff will decrease for a fact. The staff may not be mentally prepared for this change and continue to use the previous system. In such cases, transferring everything from the previous one to the new one will also give additional workload and different errors in the copying of records might also arise.


The administration should anticipate this decrease in productivity and hurdles in workflow and may require additional software support to take care of this challenge.

Some temporary staff could be hired to perform mundane work, while the vendor of the software could also be asked for live support during the implementation. The vendor needs to stay on board even after the implementation to check for any bugs and offer assistance on the spot.

Shifting the Data


The transfer of data can cause demotivation in the staff due to the monotonous work routine. Medical practices often have to decide to what extent will the historical data be copied and what will be discarded. Moreover, the sensitive and private information needs to be transferred accurately. Any errors that might occur can cause serious troubles for the practice. Hence, the practices need to be extra cautious when dealing with such sensitive data.


Practices can appoint a person in charge of all the transmission of data, who would be responsible and accountable for this whole process. This data must be saved into the newer system regularly so that the newer Cloud-based EMR System remains handy and easy for everyone.

EHR Software Implementation Costs

You pick a vendor based on your preference and you pay the fee but the story doesn’t end there. EHR Software technology comes with its own set of direct and indirect installation costs some of which are mentioned below:

Direct Costs

There are a number of factors that can affect the cost e.g.

Systems Architecture Preference

  • Cloud-Based Software

This requires an initial startup fee, monthly or annual subscription fee, extra server’s fee (in some cases), storage, data backups, and security with limitation of access.

  • Server-Based Software

This requires the purchase of a perpetual license, management of all of the back-office technology, heavy-duty servers for backup and storage and possibly a permanent IT staff.

Size and Requirement of Practice

    • Amount of Data
    • Number of access provided
    • Number of devices authorized
Cost In-Office SaaS
Upfront Cost Yearly Cost 5 Year TCO Upfront Cost Yearly Cost 5 Year TCO
Estimated Average Cost $33,000 $4,000 $48,000 $26,000 $8,000 $58,000



Indirect EHR Implementation Costs

In addition to upfront and standard EHR fees, practices also face some indirect EHR implementation costs, and they’re far from trivial. Budgeting for these investments is critical, as they represent a significant share of the overall EHR implementation budget.


Training is a necessary evil as it can be expensive, but it will help in eradicating the struggle of your staff.


To keep this under budget, practices generally go through intensive training only for non-tech-savvy employees so that they can become familiar and comfortable with the software.


After the EHR software going live creates a need for extra IT expertise for support and maintenance.


Hiring permanent staff for IT support is essential if you are opting for a server-based EMR Software. This expense can be reduced by opting for a Cloud-Based EMR and Practice Management Software that offer support through remote access.


This goes without saying that EHR Software from selection to implementation is a huge task. Every practice during and after the transition period can face unique challenges. The issues and the solutions mentioned above are not standard.

Software vendors now are developing software in modular form, offering a lot of features. Only a few of these features are actually applicable to your particular. We advise that you should appoint a person who can have a clearer understanding of the software and who is able to work closely with the EHR Software provider.

The appointed person should look at the workflow to determine the administrative and financial aspects of the EHR and also consult your provider to ensure that the software you are choosing only provides those features and not more than what you need.