Background Improving the health and well-being of young people is a public health priority. Schools present an ideal setting to implement strategies to improve young people’s health and well-being. Conducting health improvement research in schools is, however, challenging. Schools can find it difficult to participate and adhere to research processes because of competing priorities, as well as time and resource constraints. There is a lack of literature on the perspectives of school staff and other key stakeholders in young people’s health on how best to work with schools to improve health outcomes in young people. This study aimed to explore the perspectives of key stakeholders in young people’s health on how best to work with schools to conduct health research relating to young people. The study aimed to provide key practical and logistical guidance for collaborating with schools and stakeholders for school-based health research.

Methods A total of 26 semi-structured interviews were conducted with school staff (n=11, 80% female), local authority professionals (n=5, 40% female), and key wider stakeholders (n=10, 80% female), based in South West England. Interview data were analysed using the 7-stage Framework Method.

Results The three main themes identified from the data were 1) recruitment and retention; 2) practicalities of data collection in schools; and 3) collaboration from design to dissemination. The results showed that research should be collaborative with school staff and young people, consistent with school priorities and values, and flexible and tailored to school timetables and resources.

Conclusion Overall the findings demonstrated that researchers must acknowledge the role of local authorities and academy trusts in the English education system, and work closely with these when conducting school-based health research. Research should be school-led and tailored to each school, and researchers should aim to develop a collaborative learning network with schools.