Identifying the factors and components of an electronic prescription system is of utmost importance in effective designing and implementation of this system. In this regard, the current study was conducted to determine the main factors affecting the national model of electronic prescription from the physicians' point of view. This is a cross-sectional, descriptive-analytical research carried out in 2015. Based on the census sampling method, 104 members of the board of directors of the Iranian general practitioners' associations, general practitioners' alumni association of Iran, and physicians owner of a website or weblog were selected as samples for this study. Data were collected using a valid and reliable questionnaire. After analyzing the data with SPSS software (v.16), a model was proposed using a regression algorithm. The findings indicated that accessing the current medication data and medication history of patients during prescription, and also creating the electronic patient medication record (ePMR) are the most important selective components for physicians with frequency percent of 92.1%. Moreover, from the physicians' viewpoint, the method of "transmission of prescriptions to the central national database and retrieving prescriptions information from the selected pharmacy of the patient" had the highest priority (weight coefficient) in the model of the national electronic prescription system. Therefore, the Iranian prescription system is required to be developed based on the centralized architecture and national electronic prescription database.