Gender-based violence (GBV) remains a significant challenge affecting the safety and well-being of students in many educational institutions in Kenya. However, research on school-related GBV has largely focused on its social and psychological consequences, with limited attention given to its effects on students’ academic performance. This study examined the relationship between sexual forms of gender-based violence and students’ test scores in public secondary schools in Bungoma County, Kenya. The study was guided by Social Feminism Theory and Resilience Theory and adopted a correlational research design to examine the association between experiences of sexual violence and students’ academic outcomes. Stratified random sampling was used to select 184 public secondary schools from a total of 342 schools in Bungoma County. A sample of 1,104 students was selected from an estimated population of approximately 250,000 students using simple random sampling. In addition, purposive sampling was used to select 184 heads of Guidance and Counseling departments, three Sub-County Directors of Education, thirteen survivors of gender-based violence, and one County Woman Representative. Data were collected through questionnaires, interviews, and document analysis. Quantitative data were analyzed using descriptive and inferential statistics, including Pearson Product–Moment Correlation and Analysis of Variance (ANOVA), while qualitative data were analyzed thematically. The findings revealed a moderate negative correlation between sexual forms of gender-based violence and students’ test scores (r = –0.45), indicating that increased exposure to sexual violence was associated with lower academic performance. Qualitative findings further revealed that incidents of sexual violence often remain underreported due to stigma, fear of retaliation, and weak institutional response mechanisms. The study concludes that sexual gender-based violence negatively affects students’ academic performance and highlights the need for stronger prevention measures, effective reporting systems, and improved psychosocial support services within schools.