Physical literacy is crucial for children's appropriate development and physical, social and mental health. In a school setting, class-based physical activity (PA) interventions are considered to be appropriate programs to foster PA participation and cognitive development. The purpose of this project, named the Active Learning in PHYsical Literacy (ALPHYL) study, was to describe a multicomponent classroom-based physically-active learning randomised control trial (RCT) in primary school children. The main purpose was to promote children's physical literacy, academic achievement and cognitive function. The ALPHYL study is mainly based on physical literacy, active school models and the Supportive, Active, Autonomous, Fair and Enjoyable principles. The ALPHYL is an 8-10-week RCT to be conducted in six primary schools (12 classes) in Valencia (Spain) and its metropolitan area. Schools will be randomly assigned to the intervention or waiting-list control group. After a 30 h in-person training course for teachers and weekly meetings in the three months of resource preparation, the ALPHYL intervention will be conducted in physical education (PE) and non-PE lessons by teachers. The intervention consists of at least three daily sessions of physically active learning in addition to model-based PE teaching. Its feasibility will be evaluated weekly according to the Reach, Effectiveness, Adoption, Implementation and Maintenance framework. To assess its effectiveness, a pre-test, post-test and retention (8-10 weeks post-intervention) with primary outcomes (i.e., PA level, motor competence, perceived motor competence and PL, motivation, perceived social support, academic achievement and cognitive function), secondary outcomes and covariates will be collected.