Background: Poor menstrual health and hygiene (MHH) is a globally recognised public health challenge. A pilot study of an MHH intervention was conducted in two secondary schools in Entebbe, Uganda, over 9 months. The intervention included five components delivered by the implementing partner (WoMena Uganda) and the research team: (i) training teachers to implement government guidelines for puberty education, (ii) a drama skit to reduce stigma about menstruation, (iii) training in use of a menstrual kit (including re-usable pads), (iv) guidance on pain relief methods including provision of analgesics and (v) improvements to school water, sanitation and hygiene (WASH) facilities. The aim of the process evaluation was to examine implementation, context and possible causal pathways. Methods: We collected information on fidelity, dose, reach, acceptability, context and mechanisms of impact using (i) quantitative survey data collected from female and male students in year 2 of secondary school (ages 13-21; 450 at the baseline and 369 at endline); (ii) qualitative data from 40 in-depth interviews with parents, teachers and female students, and four focus group discussions with students, stratified by gender; (iii) data from unannounced visits checking on WASH facilities throughout the study; and (iv) routine data collected as part of the implementation. Quantitative data were used primarily to assess fidelity, dose and reach. Qualitative data were used primarily to assess acceptability, context and possible mechanisms.