This study aims to develop an E-learning system for the Graduate Program to address teaching-learning issues. This system is a significant tool in helping instructors, students and department heads as they can manage and monitor classes online with facility, effectiveness, and efficiency. The system for the Graduate Program includes course management, classroom management, learning management, online assessment management, monitoring message board for communication, course feedback for instructors, and virtual classroom for discussion. RAD (Rapid Application Development) was applied in developing this system. This model is a team-based technique that focuses on fast information system development for the construction of prototypes which allow users to examine a working model as early as possible, to determine if it meets their needs, and to suggest necessary changes. The model includes phases of planning, analysis, prototype cycle, design, implementation and deployment. After the system was done, a questionnaire was given to the respondents. The questionnaires were taken from ISO standard questionnaires for evaluating systems functionality, reliability, usability, efficiency, maintainability, and portability. After the evaluation was done, it was found out that all aspects of the system were rated above the average which indicates that the system complies with all the necessary functionality and features of an E-Learning System. Thus, the system can be implemented in the Graduate Program of Central Philippine University.