Electronic prescribing systems (e-prescription) for medications have many benefits, including patient safety, increase in patient satisfaction, efficiency of pharmacy work, and quality of patient care. However, few studies have been conducted to evaluate the national e-prescription system "Wasfaty" service in Saudi Arabia, which was recently adopted. The aims of this study were to explore the benefits observed through the use of the system and most frequent challenges experienced by community pharmacists in the Qassim region of Saudi Arabia. This study was conducted using a descriptive survey on a web-based platform. The target population of the study included community pharmacists in the Qassim region of Saudi Arabia who worked in pharmacy chains utilizing the e-prescription service between September 2022 and November 2022. Descriptive statistics along with multiple ordinal regression were used for data analysis. The study population consisted of 124 pharmacists, of which 62.9% (78/124) were males and 37.1% (46/124) were females. Most of the participants had a positive perception of the e-prescription system with regard to medication safety, with 68.6% (85/124) indicating that e-prescriptions reduce the risk of dispensing errors. However, 81.5% (101/124) did not agree that the e-prescription system resulted in a reduction in workload, and 70.2% (87/124) disagreed that the service increased patient satisfaction. The results of this study indicated that the national e-prescription system has many benefits to healthcare employees and improves their work, particularly for patient safety, reducing medication errors, and improving the management of patient medications. The participants believe that there is a need to improve communication with prescribers, showing concern about the unavailability of some medications; thus, it is important for policymakers to encourage other pharmacy chains and suppliers to join the service to increase patient access to medications.