School-based health promotion interventions (HPIs) are commonly used in schools, but scientific evidence about the structures of effective interventions is lacking. Therefore, we conducted a mixed methods systematic literature review to recognize the HPI structures related to their effectiveness. Based on the inclusion criteria, 49 articles were selected for the literature review. The articles, published in 2011–2022, described 46 different school-based interventions conducted in 20 different countries. The average duration of the interventions was 12 months, and they were implemented mostly with an RCT study design (61.2%) and by targeting children (69.4%). Three main groups of interventions were identified and explained: (1) extensive and long-term interventions; (2) school policy-changing interventions; and (3) highly effective interventions. Effective school-based HPIs included multiple target groups, multiple providers with external experts, and an efficient duration and timing of follow-ups. The implications for educational research and school practice are presented. Evidence on the effectiveness of health-related interventions is still lacking and needs to be addressed in further studies.