Children engage in a high volume of sitting in school, particularly in the classroom. A number of strategies, such as physically active lessons (termed movement integration (MI)), have been developed to integrate physical activity into this learning environment; however, no single approach is likely to meet the needs of all pupils and teachers. This protocol outlines an implementation study of a primary school-based MI intervention: CLASS PAL (Physically Active Learning) programme. This study aims to (A) determine the degree of implementation of CLASS PAL, (B) identify processes by which teachers and schools implement CLASS PAL and (C) investigate individual (pupil and teacher) level and school-level characteristics associated with implementation of CLASS PAL. The intervention will provide teachers with a professional development workshop and a bespoke teaching resources website. The study will use a single group before-and-after design, strengthened by multiple interim measurements. Six state-funded primary schools will be recruited within Leicestershire, UK.Evaluation data will be collected prior to implementation and at four discrete time points during implementation: At measurement 0 (October 2016), school, teacher and pupil characteristics will be collected. At measurements 0 and 3 (June-July 2017), accelerometry, cognitive functioning, self-reported sitting and classroom engagement data will be collected. At measurements 1(December 2016-March 2017) and 3 , teacher interviews (also at measurement 4; September-October 2017) and pupil focus groups will be conducted, and at measurements 1 and 2 (April-May 2017), classroom observations. Implementation will be captured through website analytics and ongoing teacher completed logs. Ethical approval was obtained through the Loughborough University Human Participants Ethics Sub-Committee (Reference number: R16-P115). Findings will be disseminated via practitioner and/or research journals and to relevant regional and national stakeholders through print and online media and dissemination event(s).