Background <p>Schools play a key role in mental health problem prevention, reaching most children during critical periods. Leveraging this opportunity requires understanding the complex system underlying school-based prevention, comprising various connections between multiple stakeholders. This study charts the structure and dynamics of a school-based mental health problem prevention system in Estonia using a novel collaborative system mapping method.</p> Methods <p>Stakeholder workshops were conducted with teachers, support specialists and school leaders to co-create system maps reflecting participants’ perceptions of the system’s actors and connections.</p> Results <p>The resulting system map identified 19 key actors, ranging from local-level organizations to state-level institutions, and four types of connections: direct prevention delivery, funding, provision of materials and training and general cooperation. Findings also revealed some challenges within the system, such as roles being distributed between many actors without clear central oversight, which leads to abundant but difficult to navigate materials and training offers. At the same time, schools emphasise a lack of sufficient guidance for engaging parents, reflecting that the system might not adapt to the needs of the schools.</p> Conclusions <p>This work highlights that enhancing the prevention system requires addressing broader issues, such as different stakeholders’ roles, partnerships and resource flows within the system. The system map can serve as a foundation for further studies exploring different perspectives on the prevention system, quantifying its properties, and identifying leverage points for system improvement.</p>