The study aimed at absenteeism and students’ academic performance of st joseph vocational secondary school Nyamityobora and it was guided by the following objectives; To assess the rate of absenteeism at St Joseph vocational secondary School, to determine the level of students' academic performance at St Joseph vocational secondary School and to examine how absenteeism affects students' academic performance at St Joseph vocational secondary School. Therefore 187 respondents were selected including 180 Students (36 from each class including class councilors), 5 class teachers, the DOS and the head teacher. After the data collection, qualitative data obtained was coded, tabulated on the scale and entered in the computer system using Statistical Package for Social Scientists. The study was carried out at St Joseph vocational secondary School located in Rubiri cell, Nyamityobora ward, kakoba Division, Mbarara municipality, mbarara district, Uganda. The study focused on the students of S.3, S.2 and S.1, class teachers, director of studies and the head teacher. The researcher found out that the major effect of absenteeism on students was poor academic performance as presented by the majority of the respondents (40.9%) with some other effects such as missing exams (22.7%), failure to meet the pass mark (15.5%), disorganization in the school program (9.5%) early pregnancy and indiscipline among learners (4.5%) and school dropout (2.8%). The administration should make a different approach to collection school fees rather than sending students home every now and then. They should always invite the parents to school and discuss about the fee’s issues.