The aim of the MENISCUS trial was to assess whether a multicomponent menstrual health intervention improved educational attainment, mental health symptoms, menstrual management and quality of life outcomes among girls in secondary school in Uganda. A total of 60 secondary schools in Wakiso and Kalungu districts were randomised, so that 30 schools received the MENISCUS intervention in 2022, and 30 received optimised usual care. The MENISCUS intervention involved 1) Training teachers to provide puberty education to boys and girls 2) Working with school drama clubs to tackle menstrual health issues, with performances to parents and teachers 3) Providing menstrual kits, including a supply of re-usable pads and optional menstrual cups with training on their use 4) Providing strategies for pain management, including vouchers for pain relief medication 5) Simple upgrades to school toilets, including providing items such as bins and soap, and repairing lock 6) Establishing a menstrual health action group at each school to oversee the delivery of the intervention. The primary outcomes were i) examination performance based on the curriculum taught during the intervention year; and ii) mental health symptoms including emotional symptoms, attention and peer relationship problems. We also assessed the impact of the intervention on other outcomes including (in both girls and boys) menstrual knowledge and attitudes; and (in girls only) menstrual practices, pain management, self-efficacy to manage menstruation, quality of life, prevalence of urinary tract infections, school and class attendance, and confidence in science and maths.