INTRODUCTION: Primary school-based physical activity interventions, such as The Daily Mile initiative, have the potential to increase children's physical activity levels over time, which is associated with a variety of health benefits. Comparing interventions or combining results of several studies of a single intervention is challenging because previous studies have examined different outcomes or used different measures that are not feasible or relevant for researchers in school settings. The development and implementation of a core outcome set (COS) for primary school-based physical activity interventions would ensure outcomes important to those involved in implementing and evaluating interventions are standardised. METHODS AND ANALYSIS: Our aim is to develop a COS for studies of school-based physical activity interventions. We will achieve this by undertaking a four-stage process:(1) identify a list of outcomes assessed in studies through a systematic review of international literature; (2) establish domains from these outcomes to produce questionnaire items; (3) prioritise outcomes through a two-stage Delphi survey with four key stakeholder groups (researchers, public health professionals, educators and parents), where stakeholders rate the importance of each outcome on a 9-point Likert scale (consensus that the outcomes should be included in the COS will be determined as 70% or more of all stakeholders scoring the outcome 7%-9% and 15% or less scoring 1 to 3); (4) achieve consensus on a final COS in face-to-face meetings with a sample of stakeholders and primary school children. ETHICS AND DISSEMINATION: We have received ethical approval from Imperial College London (ref: 19IC5428). The results of this study will be disseminated via conference presentations/public health meetings, peer-reviewed publications and through appropriate media channels. TRIAL REGISTRATION NUMBER: Core Outcome Measures in Effectiveness Trials Initiative (COMET) number: 1322.