Computer Based Testing has become a prominent method in student assessment in Nigeria and student perception on this testing technique is paramount. This study examined the perception of undergraduate students towards computer based testing by comparing several modules studied by Undergraduate students in Nigeria which constitutes a major gap in literature. Results showed that majority of students preferred computer based testing to paper based testing but were not will to adopt this technique in all courses. Results further showed majority of students showed preference to paper based tests in Mathematics more than 50% of students had below average grades when the CBT technique was implemented. Similarly, students showed poor grades in Mathematics, Chemistry and Physics, results further showed the relationship between computer and anxiety and performance in in Mathematics. This study has implications for university administrators in the creation of policies for Computer based testing.