Background: School health program (SHP) involves all aspects of the school program that contribute to understanding, maintaining, and improving school health. This study aimed to assess the level of implementation of SHP in all its domains among primary schools.Methods: The study is a comparative, cross-sectional study carried out in 64 public and private primary schools each in Ilorin Nigeria using the school health program evaluation scale (SHPES) pre-tested, self-administered questionnaire to obtain data. The data collected on the questionnaire was appropriately verified and computed for analysis.Results: A total of 128 primary schools were surveyed. Eighty-three (64.8%) of the 128 schools had school health committee. One hundred and four (81.3%) of the sampled primary schools in Ilorin had no designated health personnel. Significantly more private schools had no health hazards at the site (p=0.001) than public schools. Twenty-seven schools (21.1%) met the minimum acceptable total SHP score of 103. One hundred and seven met the minimum acceptable score of 19 in SHS. Six schools (all private) met the minimum acceptable score of 57 in HSE. Ninety-eight schools met the minimum acceptable score of 27 in SHI. 25 private schools (39.1%) performed well in the total SHP score compared with 2 (3.1%) among the public schools.Conclusions: The SHP implementation was poor in this study area. However, private schools performed better than public schools and the difference was statistically significant.