Adolescent girls face social, psychological, and physical problems managing menstruation in schools in low-resource settings. This study aimed to evaluate the social and physical menstrual health environment of secondary schools in Wakiso and Kalungu districts, Uganda, in preparation for a subsequent menstrual health intervention trial to improve education, health and wellbeing. We conducted a qualitative rapid assessment in 75 secondary schools in Uganda. This involved conducting in-depth interviews with 150 head/senior teachers and 274 students, 26 Focus Group Discussions with students, and 13 transect walks to observe school Water, Sanitation and Hygiene (WASH) facilities between May and October 2021. Due to COVID-19 related school closures, face-to-face research activities were halted and in-depth interviews were conducted over phone and replaced focus group discussions. We employed a thematic framework analysis approach using the social-ecological model (which focuses on the complex interplay between individual, interpersonal, institutional, and societal factors) to generate themes and key concepts. Participants described the social and physical menstrual health environment of secondary schools at the individual level (knowledge gaps on menstruation before menarche, negative norms and beliefs about menstrual health); interpersonal level (limited psycho-social support, myths and misconceptions about the disposal of sanitary materials and pain relief, menstrual hygiene management (MHM) support from school nurses, peers and senior teachers); institutional level (non-implementation of Government circulars on MHM, lack of school-level guidelines policies and programs on MHM and poor WASH facilities, i.e. lack of soap, safe water and unclean toilets); and societal level (MHM programmes provided by civil society groups, health workers, and students' school associations). The findings showed individual, societal and institutional burdens related to menstrual experiences. Multi-level evidence-based interventions aimed at improving the social and physical environment for menstrual health among school-going girls are needed.