Background: Schools are ideal environments in which to conduct child and adolescent physical activity (PA) research. Despite this, PA-specific practical guidance for school-based research is lacking, which may present unique challenges to researchers. Based on reflections from our own experiences, this paper seeks to provide practical guidance on how best to approach school-based PA data collection. Discussion: This paper focuses on the practicalities of quantitative and qualitative data collection in English primary (4-11 years) and secondary (11-16 years) schools. Recruitment and consent are discussed, and practical guidance provided with respect to engagement with parent/carer(s) and ethical considerations. The importance of good communication with schools, together with its importance in facilitating efficient data collection (through planning, data collection and resource utilisation), is described. Finally, the importance of giving back to the school and participants once a research project has been completed is stressed. Summary: Improved understanding of data collection procedures for school-based PA research is key to helping research become more systematic and efficient. Findings in this paper will be particularly useful to undergraduate and postgraduate students and early career researchers.