The available modes of fees payment to Makerere University through Cash Deposits, Electronic Funds Transfer and Bank Drafts have caused long queues, students missing to sit for their tests and examinations, and loss of money intended for fees while waiting to reach bank counters to make payments among others. The problem is addressed by developing a system(MUK-OFPS) that enables students and their sponsors to securely pay university fees online from wherever they are using credit and debit cards. The study focused on the development of a web based system that allows online fees payment. Students and their sponsors will use the system to pay all kinds of university fees online, and by the university accountants to verify these payments. Literature asserts that, for nearly every business, the simple act of collecting payments from consumers is actually quite complex and yet organizations want to make it easy and convenient for customers to pay, so they offer multiple choices of payment types and channels. This will reduce the lengthy queues, congestion at banks and reduce the number of students that currently miss sitting for their exams at the University.