This study focuses on the relationship between menstruation and the schooling experience of female adolescents in Peru from an ecological and gender approach. Qualitative data were collected from rural and urban areas through individual interviews and participatory activities with 277 participants, including adolescents and key informants. The participants were chosen through convenience sampling in 11 schools. The results were tripartite: (1) most adolescents experience fear and shame related to menstruation because of gender meanings about the menstrual body; (2) there is bullying and aggression associated with menstruation by male peers in the school grounds; and (3) the issues of menstruation in the institutional context are not sufficiently addressed in public policy, teacher training and provision of sanitation facilities. Therefore, a critical revision of the gender norms that place female adolescents at a disadvantage in school grounds is urgent in addition to improving water and sanitation infrastructure and maintenance.