Enterprise architecture (EA) is a tool that aligns organization’s business-process with application and information technology (IT) through EAmodels. This EA model allows the organization to cut off unnecessary IT expenses and determines the future and current IT requirements and boosts organizational performance. Enterprise architecture may be employed in every firm where the firm or organization requires configurations between information technology and business functions. This research investigates the role of enterprise architecture in healthcare organizations and suggests the suitable EA framework for knowledge-based medical diagnostic system for EA modeling by comparing the two most widely used EA frameworks. The results of the comparison identified that the proposed EA has a better framework for knowledge-based medical diagnostic system.