This paper proposes a methodology for evaluating the portfolio of projects of a program funded by the Fondo de Ciencia Tecnología e innovación, case study: "Investigación Técnico-Social de Oleaginosas Promisoras con miras a su Desarrollo Agroindustrial". To this end, different methods of evaluating projects presented in the specialized literature, taking into account the specificities of the case study were studied. The Process of Hierarchical Analysis (AHP) was selected as the best option, giving a weighting to the criteria and sub-criteria proposed in the hierarchical structure and a scoring for the 15 sub-projects that make up the portfolio. For the mathematical development of the methodology proposed Super Decisions Software was used. The weights were calculated in Excel and the Survey Monkey tool for gathering the information is used. The three sub-criteria with more weight were respectively: human resources, technical feasibility and articulation of actors and the criteria were: feasibility, resources and benefits. Among the projects with the best final scores were social projects.