IntroductionExcess free sugar intake is associated with obesity and poor dental health. Adolescents consume substantially more free sugar than is recommended. National (UK) School Food Standards (SFS) are in place but are not mandatory in all schools, and their impact on the diets of secondary school pupils is unknown. We aim to evaluate how SFS and wider healthy eating recommendations (from the national School Food Plan (SFP)) are implemented in secondary schools and how they influence pupils’ diets and dental health.Methods and analysisSecondary-level academies/free schools in the West Midlands, UK were divided into two groups: SFS mandated and SFS non-mandated. Using propensity scores to guide sampling, we aim to recruit 22 schools in each group. We will compare data on school food provision and sales, school food culture and environment, and the food curriculum from each group, collected through: school staff, governor, pupil, parent surveys; school documents; and observation. We will explore the implementation level for the SFS requirements and SFP recommendations and develop a school food typology. We aim to recruit 1980 pupils aged 11–15 years across the 44 schools and collect dietary intake (24-hour recall) and dental health data through self-completion surveys. We will compare free sugar/other dietary intake and dental health across the two SFS groups and across the identified school types. School type will be further characterised in 4–8 case study schools through school staff interviews and pupil focus groups. Evaluation of economic impact will be through a cost-consequence analysis and an exploratory cost–utility analysis.Ethics and disseminationEthical approval was obtained from the University of Birmingham Ethical Review Committee (ERN_18-1738). Findings will be disseminated to key national and local agencies, schools and the public through reports, presentations, the media and open access publications.Trial registration numberISRCTN 68757496 (registered 17 October 2019).