Abstract: Variations in the academic performance among students at all levels of education are one issue for years now that has attracted the attention of many  researchers across the globe. This has prompted researchers and educationists to find out what factors or reasons can be attributed to these variations. Numerous studies have been conducted to determine the various reasons to explain this cause. The purpose of this study therefore, was to compare the academic performance of students in the Bachelor’s degree of Information Technology (BIT) having Arts and Science backgrounds in universities of Uganda. In order to achieve the objective of this study, a sample of 202 final year BIT students were purposively selected from two universities in Uganda. These students were categorized on the basis of their A’ level backgrounds (130 Arts and 72 Sciences). A descriptive approach employing the Welch’s t-test was used to determine the difference between the performance of the two groups and a simple linear regression analysis was used to examine the correlation among students’ performance between semesters. The results indicated that there’s a significant difference in the academic performance of the two groups, with the science group outperforming arts. However, it was found that there is a more linear increase in the performance of Arts students from semester one through semester five. Furthermore, Arts students performed slightly better than Science counterparts in some course units. Thus the study concludes that Science students perform better than Arts students in the overall semester final examination with Arts students having room for improvement in their performance.