INTRODUCTION: Smoke-free school hours (SFSHs) entails a smoking ban during school hours and might be an effective intervention to reduce the high smoking prevalence in vocational schools. For SFSH to be effective, the policy must be adequately implemented and enforced; this challenge for schools constitutes a research gap. The 'Smoke-Free Vocational Schools' research and intervention project has been developed to facilitate schools' implementation of SFSH. It is scheduled to run from 2018 to 2022, with SFSH being implemented in 11 Danish vocational schools. This study protocol describes the intervention project and evaluation design of the research and intervention project. METHODS AND ANALYSIS: The intervention project aims to develop an evidence-based model for implementing SFSH in vocational schools and similar settings. The project is developed in a collaboration between research and practice. Two public health NGOs are responsible for delivering the intervention activities in schools, while the research partner evaluates what works, for whom, and under what circumstances. The intervention lasts one year per school, targeting different socioecological levels. During the first 6 months, activities are delivered to stimulate organisational readiness to implement SFSH. Then, SFSH is established, and during the next 6 months, activities are delivered to stimulate implementation of SFSH into routine practice. The epistemological foundation is realistic evaluation. The evaluation focuses on both implementation and outcomes. Process evaluation will determine the level of implementation and explore what hinders or enables SFSH becoming part of routine practice using qualitative and quantitative methods. Outcomes evaluation will quantitively assess the intervention's effectiveness, with the primary outcome measure being changes in smoking during school hours. ETHICS AND DISSEMINATION: Informed consent will be obtained from study participants according to the General Data Protection Regulation (GDPR) and Danish data protection law. The study adheres to Danish ethics procedures. Study findings will be disseminated at conferences and further published in open-access peer-reviewed journals.