Background There is general agreement that sexuality is a central aspect of human development; it is key in sexual health and reproductive education during adolescence. However, in spite of the existing interventions on this topic and the evidence generated, the inclusion of a gender focus in sexuality is relatively recent and there is little evidence available, thus structured and corroborated interventions with a gender-transforming perspective in sexuality are required.Methods We will use a mixed method experimental design with a parallel cluster-randomized trial (GRTs) that will evaluate the effectiveness of a comprehensive gender-transformative intervention of sexual education (ENFOCATE -Focus-on-), which will be complemented with qualitative studies to understand the implementation process. The participants will be 609 10th and 11th-grade students. The randomization will be by grade, and the data will be collected at three moments (pre-intervention, post-intervention, and a 3-month follow-up).Discussion Comprehensive, gender-focused, and culturally pertinent interventions in sexuality are needed for adolescents of countries with high, middle, and low incomes. These produce better results in terms of sexual health, and including a gender-transformative focus contributes to equity in health. Focus-on is unique since it uses a comprehensive gender-transformative intervention in sexual education that will allow putting into practice a program based both on international evidence and that which arises from the object population. It also uses a culturally-sensitive focus, since it is designed based on the characteristics of the object population; it will allow adapting some activities to the needs of the context in which it is developed.Trial registration The study was prospectively registered on June 6, 2023, at ClinicalTrials.gov ID: NCT05896540. Protocol version number 1.0. May 22, 2023.