Health-promoting schools have been associated with improvements in the health status of students globally. This study is a secondary analysis study assessing Iranian HPSs. This was a cross-sectional study on routinely collected data using an external audit 63-item checklist, which was utilized to evaluate 440 HPSs between 2014 and 2017. The mean score for each of the checklists’ components was calculated. Nonparametric tests were conducted to investigate the association between the presence of a school caregiver, students’ educational level and the school’s score. While the number of five- and four-star schools increased significantly, one- to three-star schools declined. Providing clinical and counseling services had negative growth. Despite the steady growth of the staff’s health, this category still had the lowest score among; on the contrary, physical activity had the highest score in 2017. The presence of a full-time school caregiver and middle schools were both significantly correlated with achieving higher scores (p < 0.005). It seems that in addition to developing school facilities to promote physical activities, measures should be taken to promote access to counseling services, considering health issues of students and staff and finally increasing the number of full-time school caregiver.