Adolescents in Panama face multiple barriers that affect their health, such as high rates of teenage pregnancy, increased human immunodeficiency virus (HIV) infections and sexual violence. Equal relationships between women and men are likely to reduce such risks. Here, we suggest that the school-based enhancement of Social and Emotional Learning core competencies—awareness of self and others, positive attitudes and values, responsible decision-making, and social interaction skills—could foster positive changes in behaviors between boys and girls, specifically through a focus on equal roles, equal rights in relationships and nonviolent problem solving. This paper, using the Intervention Mapping Protocol, describes the process of development of, and planning surrounding the implementation and evaluation of the program ‘Me and My new World’, a Social Emotional Learning intervention for middle school students (12–15 years old) in Panama. Program development was based on a needs assessment (Araúz Ledezma et al. (2020) Behavioural and environmental influences on adolescent decision making in personal relationships: a qualitative multi–stakeholder exploration in Panama. Health Education Research, 35, 1–14.) and a literature review of theory- and evidence-based Social and Emotional Learning (SEL)-programs. Intervention outcomes, performance objectives and change objectives of the intervention were identified. The practical applications of different theory-based methods allowed for contextual considerations that could potentially influence the expected behavioral outcomes of the intervention. Teachers were the implementers of the program, and during development, implementation, and evaluation, the roles, opinions, and teaching methods of all stakeholders were recognized. We conclude that Intervention Mapping allows for the analysis of multiple factors influencing the development and implementation of Social Emotional Learning programs promoting equal relationships among adolescents in a developing country, with a special consideration of culture, educational systems, and policies, from a capability development perspective.