This study developed a series of recommendations for electronic health record system (EHR) implementation for the medication administration process within small-scale rural healthcare facilities. To establish a series of the EHR implementation preparation guidelines for the medication administration process in the rural healthcare facilities, focus groups were used to elicit the nurses' concerns in implementing the new EHR system for the medication administration during training sessions for the new system. This study compared the potential errors in the medication administration process before and after implementing the EHR system to demonstrate its impacts for healthcare practices. The results showed that the IT system indeed changed the workflow for passing out medications at the rural hospitals. A series of recommendations were suggested to eliminate the problems in the process, such as, prevent unnecessary interruptions, establish clearly and proper standards, optimize software interface and operations, provide proper medication preparation area, and optimize mediation restock schedules, etc.