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Trial registration: ClinicalTrials.gov identifier: NCT03894241 Date of register: March 28, 2019. Retrospectively Registered., Cogni-Action Project is supported and the study protocol was peer reviewed by the National Commission for Scientific and Technological Research CONICYT/FONDECYT INICIACION 2016 grant no. 11160703. PS-U was supported by a grant from CONICYT/BECAS Chile/72180543. IE-C is supported by a grant from the Spanish Ministry of Science and Innovation (IJCI-2017-33642). CC-S is supported by a grant from the Spanish Ministry of Economy and Competitiveness (BES-2014-068829). JHM and JMG are supported by the Spanish Ministry of Education, Culture and Sport (FPU15/ 02645, FPU14/06837, respectively). Funding bodies has no role in the design of the study and collection, analysis and interpretation of data and in writing the manuscript. This work is part of Ph.D. Thesis conducted in the Biomedicine Doctoral Studies of the University of Granada, Spain., Background: Education and health are crucial topics for public policies as both largely determine the future wellbeing of the society. Currently, several studies recognize that physical activity (PA) benefits brain health in children. However, most of these studies have not been carried out in developing countries or lack the transference into the education field. The Cogni-Action Project is divided into two stages, a cross-sectional study and a crossover-randomized trial. The aim of the first part is to establish the associations of PA, sedentarism, and physical fitness with brain structure and function, cognitive performance and academic achievement in Chilean schoolchildren (10–13 years-old). The aim of the second part is to determinate the acute effects of three PA protocols on neuroelectric indices during a working memory and a reading task. Methods: PA and sedentarism will be self-reported and objectively-assessed with accelerometers in a representative subsample, whilst physical fitness will be evaluated through the ALPHA fitness test battery. Brain structure and function will be assessed by magnetic resonance imaging (MRI) in a randomized subsample. Cognitive performance will be assessed through the NeuroCognitive Performance Test, and academic achievement by school grades. In the second part 32 adolescents (12–13 year-old) will be cross-over randomized to these condition (i) “Moderate-Intensity Continuous Training” (MICT), (ii) “Cooperative High-Intensity Interval Training” (C-HIIT), and (iii) Sedentary condition. Neuroelectric indices will be measures by electroencephalogram Discussion: The main strength of this project is that, to our knowledge, this is the first study analysing the potential association of PA, sedentarism, and physical fitness on brain structure and function, cognitive performance, and academic achievement in a developing country, which presents an important sociocultural gap. For this purpose, this project will use advanced technologies in neuroimaging (MRI), electrophysiology (EEG), and eye-tracking, as well as objective and quality measurements of several physical and cognitive health outcomes. Trial registration: ClinicalTrials.gov identifier: NCT03894241 Date of register, National Commission for Scientific and Technological Research CONICYT/FONDECYT INICIACION 2016 grant no. 11160703, Grant from CONICYT/BECAS Chile/72180543, Spanish Ministry of Science and Innovation (IJCI-2017-33642), Spanish Ministry of Economy and Competitiveness (BES-2014-068829)