BACKGROUND: Coronavirus disease 2019 (COVID-19) pandemic in March 2020 led to new restrictive policies in several countries, including Indonesia. The comprehensive school health (CSH) framework provides overall guidance for interventions most effective in achieving specific outcomes related to health, nutrition, and education, and creating CSH programmes that account for the main contextual variations in Indonesian communities and schools is important. This study aimed to clarify how school health-related policies made before and after the COVID-19 pandemic responded to COVID-19 control measures on Lombok Island, Indonesia. METHOD: This was a qualitative observational analytic study. Researchers reviewed and analysed school health policy, held separate confirmation discussions and interviews with stakeholders and key informants, and observed policy implementation at public and private schools in Mataram. RESULTS: The analysis found weaknesses and opportunities. Weakness included lack of guidelines, comprehensive planning, inconsistent hierarchy of roles and responsibilities, and social and cultural barriers. Opportunities included the importance of funding for consistent CSH implementation, monitoring and evaluation system, implementation between public and private schools, and decentralisation. Positive findings included CSH policy integration into teaching and learning activities, regular healthy school competition program, teachers as role models, existing coordination and distribution of responsibilities between relevant stakeholders, and authorising schools to make needed adjustments. Factors influencing school health efforts included curriculum, school organisation, personal ethos, and healthcare provider partnerships. To effectively promote school health efforts, schools must assess existing health problems within the school environment and surroundings, organisational structure and capabilities including knowledge and skills, commitment, and leadership aspects. CONCLUSION: The COVID-19 pandemic has prompted the implementation of CSH policies in schools of Lombok Island, demonstrating flexibility and dedication to student welfare. Despite confusion due to changing regulations, collaboration with local health organisations and community support has resulted in effective policy implementation.