After analysis and designing the project, the researcher getting the solution of the problems of time consuming to the parent for coming to present payment tuition from bank to the APAER accountant, slow recording, weakness of processing and retrieval of students records, queuing line system that take more time to be served . The main objective of the new system is to design and develop system that will manage school fees paid by student, parents or sponsors. Electronic payment school management system will provide solution to the accountant of APAER such as school fees management, data related to the students of the school. The methodology used was waterfall model because it is very simple to understand and use. In waterfall, each phase must be completed in its entirety before the next phase can begin. At the end of each phase, a review takes place to determine if the project is on the right path and whether or not to continue or discard the project. The techniques that will be applied to achieve the specific objectives are interview, questionnaire, documentation, system analysis, system design and data modeling.