Background There is a need for interdisciplinary research to better understand how pedagogical approaches in primary physical education (PE) can support the linked development of physical, cognitive and affective aspects of physical literacy and physical activity behaviors in young children living in deprived areas. The Skill Acquisition Methods fostering Physical Literacy in Early-Physical Education (SAMPLE-PE) study aims to examine the efficacy of two different pedagogies for PE, underpinned by theories of motor learning, to foster physical literacy. Methods SAMPLE-PE will be (...) evaluated through a cluster-randomized controlled trial targeting 5–6 year old children from schools located in areas of high deprivation in Merseyside, North-West England. Schools will be randomly allocated to one of three conditions: Linear Pedagogy, Non-linear Pedagogy, or Control. Non-linear and Linear Pedagogy intervention primary schools will receive a PE curriculum delivered by trained coaches over 15 weeks, while control schools will follow their usual practice. Data will be collected at baseline (T0), immediately post-intervention (T1), and 6 months after the intervention has finished (T2). Children’s movement competence is the primary outcome in this trial. Secondary outcomes include physical activity, perceived competence, motivation, executive functions, and self-regulation. An extensive process evaluation will also examine implementation factors such as intervention context, reach, dose, fidelity and acceptability. Discussion The SAMPLE-PE project will enable better understanding surrounding how to operationalise physical literacy through enrichment of PE practices in early PE. The study will provide robust scientific evidence regarding the efficacy of underpinning PE pedagogy with theories of motor learning to promote the development of physical literacy. Trial Registration Retrospectively registered on 5th September 2018 at ClinicalTrials.gov, a resource provided by the U.S. National Library of Medicine (Identifier: NCT03551366). (shrink)