Background The onset of menstruation is a landmark event in the life of a young woman. Yet the complications and challenges that can accompany such an event have been understudied, specifically in resource-poor settings. As interventions aim to improve female attendance in schools, it is important to explore how menstruation is perceived and navigated by girls in the school setting. This research conveys rural Kenyan schoolgirls' perceptions and practices related to menstruation Methods Data were collected at six rural schools in the Nyanza Province of Western Kenya. Using focus group discussions, in-depth interviews, and field notes from observations, researchers collected information from 48 primary schoolgirls and nine teachers. Systematic analysis began with a reading of transcripts and debriefing notes, followed by manual coding of the narratives. Results Focus group discussions became opportunities for girls to share thoughts on menstruation, instruct one another on management practices and advise one another on coping mechanisms. Girls expressed fear, shame, distraction and confusion as feelings associated with menstruation. These feelings are largely linked to a sense of embarrassment, concerns about being stigmatized by fellow students and, as teachers explained, a perception that the onset of menstruation signals the advent of a girl's sexual status. Among the many methods for managing their periods, girls most frequently said they folded, bunched up or sewed cloth, including cloth from shirts or dresses, scraps of old cloth, or strips of an old blanket. Cloth was reported to frequently leak and cause chafing, which made school attendance difficult particularly as the day progressed. Attitudes and practices of girls toward menstruation have been arranged into personal, environmental and behavioural factors. Conclusion Further research on menstrual management options that are practical, sustainable and culturally acceptable must be conducted to inform future programs and policies that aim to empower young girls as they transition into womanhood. Stakeholders working within this and similar contexts must consider systematic mechanisms to explain to young girls what menstruation is and how to manage it. Providing sanitary supplies or guiding girls on how to create supplies serve as critical components for future interventions.