What can be done to promote the academic success of learners? More than a question, it is a major challenge of our time. In this perspective, metacognition seems to be a way to empower learners to take ownership of their academic success. Considering the recommendations established in the literature, we co-constructed with teachers a metacognitive educational program, called Cogni'Scol, based on brain functioning in learning. Its benefits were determined through a longitudinal study focusing on the academic success of French students. We followed sixth grade students over a two-year period who either benefited or not from a weekly session of the Cogni'Scol program. Results showed a significant effect on students' knowledge and representations of brain functioning but not on the students' academic performances mediated by improvements in their metacognition. We conclude with pragmatic reflections for researchers and educational professionals interested in the implementation of educational programs based on brain functioning in learning.