Naikuru Secondary School has a large number of students who pay all the fee through cash deposits, electronic funds transfer or bank drafts to the school’s accounts in specific bank branches. These methods of paying fees have not been efficient enough especially during periods of tests and examinations when most of the students were paying fees to meet the requirements for entering examination rooms. The process of paying fees is characterized by long queues, too much waiting by students and congestion at banks where payments were made. This has always resulted in students missing to sit for their tests and/or examinations while they were queuing to make payments. It was upon such background that the researchers embarked on the project to develop of an alternative system that enables online fees payment by students and their sponsors. With the use of questionnaires, interviews, observation and document reviews, data was collected from project stakeholders and analysed. Data flow diagrams and Entity relationship diagrams were used to accomplish system analysis and design. The system was implemented using Apache web server, Mysql database server, Hypertext Preprocessor, Hypertext markup language, Cascading style sheets and JavaScript. System testing and validation was also done by allowing users of the system interact with it using test data. Findings showed that most of the students were unsatisfied with the current modes of paying fees to the school agree that an online fees payment system can improve the process of fees payment. The result of the project was an online fees payment system for Naikuru Secondary School School(NSS-FMS) and researchers recommend the School to implement the system that provides relief of the long endured problems of the current modes of payment at the school.