The study is aimed at assessing the perceptions of male and female students on manual and online course registration systems in tertiary institutions in Nigeria. One research question was formulated to guide the study. A questionnaire containing 20 items on assessing the perceptions of students on manual and online course registration was drawn. This was validated by experts in test and evaluation in Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria. The instrument was tested for reliability using the test re-test method. The data collected was analysed using the Pearson Product Moment Correlation Coefficient and it was established at 0.88 which shows that the instrument is reliable--750 male and 750 female students were randomly selected from 3 notable Universities in the 3 regions in Nigeria. The data collected from the administered questionnaire was analysed using the t-test statistics and mean (X[line over top]) scores as well as standard Deviation (SD). It was discovered that there is no significant difference in the perceptions of male and female students on manual and online course registration systems. The respondents hold that online registration saves time, it is cost effective, information can easily be retrieved, high storage capacity, easily accessible and it is in line with the digital age. The manual registration only encourages mutual cooperation among students and errors made can be easily corrected. Suggestions were made for better improvement of online course registration system.