Little information is available regarding the influence of the interplay between the school context and school health promotion on educational performance. Therefore, we examined whether the variation between primary and secondary schools regarding the educational performance of students could be explained by general school characteristics, school population characteristics, and school health promotion and to what extent these factors interact. We performed multilevel analyses using existing data on 7021 primary schools and 1315 secondary schools in the Netherlands from the school years 2010-2011 till 2018-2019. Our outcomes were the final test score from primary education and the average grade of standardized final exams from secondary education. School health promotion was operationalized as having obtained Healthy School (HS) certification. For the test score, 7.17% of the total variation was accounted for by differences at the school level and 4.02% for the average grade. For both outcomes, the percentage of disadvantaged students in a school explained most variation. HS certification did not explain variation, but moderated some associations. We found small to moderate differences between schools regarding educational performance. Compositional differences of school populations, especially socioeconomic status, seemed more important in explaining variation in educational performance than general school characteristics and HS certification. Some associations were moderated by HS certification, but differences remained small in most cases.