Childhood overweight and psychosocial issues remain significant public health concerns. Schools worldwide implement health promotion programs to address these issues and to support the physical and psychosocial health of children. However, more insight is needed into the relation between these health-promoting programs and the Body Mass Index (BMI) z-score and psychosocial health of children, while taking into account how school factors might influence this relation. Therefore, we examined whether the variation between primary schools regarding the BMI z-score and psychosocial health of students could be explained by school health promotion, operationalized as Healthy School (HS) certification, general school characteristics, and the school population; we also examined to what extent the characteristics interact. The current study had a repeated cross-sectional design. Multilevel analyses were performed to calculate the variation between schools, and to examine the association between HS certification and our outcomes. Existing data of multiple school years on 1698 schools were used for the BMI z-score and on 841 schools for psychosocial health. The school level explained 2.41% of the variation in the BMI z-score and 2.45% of the variation in psychosocial health, and differences were mostly explained by parental socioeconomic status. Additionally, HS certification was associated with slightly lower BMI z-scores, but not with psychosocial health. Therefore, obtaining HS certification might contribute to the better physical health of primary school students in general. This might indicate that HS certification also relates to healthier lifestyles in primary schools, but further research should examine this.