Many studies have been conducted on menstrual hygiene all over the world. However, Menstrual Hygiene Management remains the problem amongst the adolescents especially in the rural lowincome countries like Uganda, particularly in its relation to school absenteeism. This study examined the effect of menstruation on academic performance among teenage girls within Rugombe Town council, Kyenjojo District. The study focused on three specific objectives namely, to assess the effects of menstrual crumbs on the academic performance of the girls, to determine the hygiene management skills in relation to academic performance and lastly to explore the social and infrastructure support system about menstruation that affect their academic performance. A simple random sampling method was employed in which three purposively selected rural public primary schools namely: Rwentuuha primary school, Buhemba primary school and Buhemba primary school, both are mixed oriented schools. The sampled data consisted of 40 female students aged between 9-11 and 110 students aged between 11-15 using a structured questionnaire. The SPSS was used to analyze the data with the aid of descriptive analysis to analyze the qualitative data collected. The study found out that at menarche it was so challenging considering some did not understand the changes. Some experienced fear and embarrassment since they lacked early training, lack of support system, money to purchase sanitary towels and lack of accurate information about menstruation both at home and in school. The study recommends that there should be early education to inform the girls. The girls should be empowered to appreciate their natural girlhood because it is their human nature. It further recommends that there should be an urgent need of breaking the silence on menstruation.