Abstract Background Schools can play a significant role in promoting health of the school community. Process evaluation is always needed to gain valuable insights on how next health promotion interventions could be improved. In Greece, the first effort to organize health education interventions in the schools at national level, was in 2019 by the Ministry of Health. The aim of the current study was to evaluate the process of a national school health education program in Greece. Methods The health education interventions took place during school year 2019-2020. They included the following themes: oral health, healthy eating, mental health, sexual health, bullying, and online safety. Multidisciplinary teams co-developed all health education material. A representative sample of teachers and health professionals filled in the structured questionnaires developed for the current study, after their informed consent. Statistical analysis was conducted using SPSS statistical software (version 22.0). Results Most teachers evaluated as excellent (83.6%) the cooperation with the school principal and the health education coordinator (77.6%), while the general satisfaction from the intervention was evaluated as excellent by 69.8% of them. In addition, most of the health professionals (90.7%) perceived as excellent the cooperation with the health education coordinator and the other health professionals (86.3%) as well as the cooperation with the school principal (87%). Conclusions Even though this was the first effort in Greece to organize school health education interventions at a national level, the results of the process evaluation have been positive. Therefore, the Greek Ministry of Health has adopted this program which is implemented until today. Key messages • Process evaluation of school health education interventions is important to improve future initiatives. • Centrally organized school health education interventions may be the key for their success.