Implementing comprehensive health promotion programs in the school setting can be challenging, as schools can be considered complex adaptive systems. As a first step towards understanding what works in improving implementation for which schools and under which conditions, this study aimed to examine the degree of implementation of health promoting school (HPS) programs, in terms of five dimensions of fidelity (adherence, dose, participant responsiveness, quality of delivery and program differentiation), and the dimensions of adaptation and integration. The HPS Implementation Questionnaire was distributed among ± 2400 primary, secondary, secondary vocational and special needs schools in the Netherlands. Employees of 535 schools (22.3%) filled out the questionnaire. Data were analysed by descriptive statistics and ANOVA tests. The average degree of implementation was 2.55 (SD = 0.58, range = 0.68-3.90; scaled 0-4). The lowest scores were achieved for participant responsiveness and adherence, and the highest for integration and adaptation. Schools that identified as HPS reported significantly higher overall degree of implementation, adherence, dose, participant responsiveness, program differentiation and adaptation than schools that didn't. Primary schools achieved a significantly higher degree of implementation, dose, participant responsiveness, quality of delivery and integration than other school types. In conclusion, many schools work on student health and well-being to some extent, but the vast majority have much room for improvement. Higher implementation scores for schools that identified as HPS underline the value of HPS programs. A broader perspective on health and more insight into conditions for effectiveness and implementation in secondary and secondary vocational schools are needed.