There are more than 1.5 million children and young people in England with special educational needs (SEN), with over 160,000 young people in the United Kingdom attending a special school or alternative provision (AP) setting. Young people with SEN have been found to be at risk for poorer mental health and well-being than non-SEN peers. However, there is a range of both school-related and research challenges associated with identifying difficulties in a timely manner. This Delphi study aims to determine a list of stakeholder priorities for improving school-based measurement of mental health and well-being among young people with SEN, at an aggregated level, within secondary special school or AP settings. A secondary objective is to inform the implementation of school-based well-being surveys, improve engagement in special schools or AP settings, and improve survey response rates among children and young people with SEN. A mixed methods Delphi study will be conducted, including a scoping review and preliminary focus groups with school staff members and researchers to establish key issues. This will be followed by a 2-round Delphi survey to determine a list of stakeholder priorities for improving the measurement of mental health and well-being at an aggregate level within special schools and AP settings. A final stakeholder workshop will be held to discuss the findings. A list of recommendations will be drafted as a report for special schools and AP settings. The study has received ethical approval from the University College London Research Ethics Committee. The stage 1 scoping review has commenced. Recruitment for focus groups will begin in Autumn 2024. The first round of the Delphi survey will commence in early 2025, and the second round of the Delphi survey in the spring of 2025. The final workshop will commence in mid-2025 with final results expected in late 2025. There is a need for clear recommendations for special schools and AP settings on priorities for improving the measurement of mental health and well-being problems among young people with SEN. There is also a need for recommendations to researchers implementing school-based well-being surveys, including the #BeeWell program, to enable them to improve their engagement in special schools and AP settings and ensure surveys are accessible. PRR1-10.2196/58610.