Gender based violence is violence directed against a person because of that person’s gender. If refers to a global phenomenon that knows no geographical, ethnic, economic, social, cultural or other boundaries. School related gender based violence or abuse is based on gendered stereotypes that targets pupils based on their sex, sexuality or gender identities. GBV happens around all societies and symbolizes a brutal violation of human rights most especially for the weaker sex. It also happens in schools where parents and guardians feel that their children are safe and protected. Therefore, the study aimed at analyzing the effects of Gender-based violence on female pupils in Kasama District at some selected secondary schools. The study adopted a mixed methods approach which is a combination of quantitative and qualitative data. The sample involved a total of 110 respondents which included; three (2) officers from Kasama Central Police Station, three (3) head teachers, fifteen (15) teachers, fifteen (15) members of the community and seventy-five (75) pupils. The respondents were obtained through purposive and simple random sampling. Data was obtained through interviews and questionnaires from the selected secondary schools. Data analysis consisted of content analysis of the interview responses and item analysis of the questionnaire responses; the data gathered was analyzed according to the themes of the study and the order of the research objectives. Data generated from the questionnaires was analyzed manually by using the Statistical Package for Social Sciences (version 26) and Microsoft Excel (version 16) to come up with frequency tables, pie charts and bar graphs to analyze data. The findings indicated that GBV causes poverty, abuse of alcohol, food scarcity, gender stereotype and early marriages. Additionally, the findings also showed that GBV had an effect on the female pupils such as; poor academic performance, absenteeism, high levels of drop-out, increased rates of illiteracy and bullying of fellow pupils.