The paper examined Electronic Payment Systems and fees Collection In Nigerian Universities using the University of Lagos, Lagos as a case study. Faced with transactional challenges such as incomplete transactions, difficulties in tracing payments, high bank charges etc., the researcher seeks to examine the various channels for electronic fees payment, challenges in using the electronic fees channel and the effects of electronic fees payments on the select Universities for the study.
Concerning methodology, both primary and secondary sources of data was used for the study. Well-structured questionnaires were distributed to respondents in both Universities and this formed the primary source of data for the study while, journals and text books were reviewed as secondary sources of data for the study. Findings from the study reveals that at a significance level of 0.05, there is a statistically significant effect between electronic fees payment and fees collection in the two Universities used for the study. Recommendations from the study includes; improvement in power supply for both Universities, re-training of staff on the various electronic channels used for fees payment, strengthening of internet services and providers around the campuses.