Adolescence is a critical time for growth and development, but this age group is often neglected in research and development of nutrition interventions. Despite recommendations from the WHO to provide nutrient supplements to adolescents, evidence remains scarce on the most effective supplementation strategy. This study aims to compare weekly iron and folic acid (IFA) supplementation with daily multiple micronutrient supplementations (MMSs) in prevention of anaemia and improvement of school outcomes among adolescents in Burkina Faso and Tanzania. A three-arm cluster randomised, school-based supplementation trial will be conducted among 84 schools (42 schools per site) and roughly 4500 students aged 10-17. Schools will be matched on three characteristics: number of students, school ranking profile, distance to main road (Tanzania) or distance to city council (Burkina Faso). Each school will be randomised to receive either weekly IFA, daily MMSs or serve as a control. Supplements will be delivered to students by teachers, who will provide monitoring data to the study team. Baseline and endline surveys will be conducted prior to and after each supplementation cycle (12 weeks in Burkina Faso; 1 year in Tanzania) to assess haemoglobin, anthropometry and sociodemographic variables. The primary outcome of haemoglobin will be analysed continuously using linear regression, and anaemia status will be analysed using logistic or multinomial regression, depending on categorisation level of the outcome. Secondary analyses of school performance indicators will also be conducted with either logistic or linear regression.