Introduction: School-based health promotion interventions (SHPI) have been introduced extensively over the last decades, but their implementation and evaluation still present challenges. Among these, the complexity of the environments in which SHPI are implemented, and intersectoral collaboration to promote more sustainable change, must be better addressed within evaluation processes. Objectives: The objectives of this study were to (1) identify pertinent scientific literature on the implementation processes for intersectoral SHPI and (2) develop a programme theory that maps potential elements of context and underlying mechanisms that may influence intersectoral SHPI. Method: A critical interpretative synthesis was performed of elements of context and underlying situational and transformational mechanisms. These were identified based on the scientific literature published between 1997 and 2017 addressing intersectoral SHPI. Results: Six potential elements of context, seven potential situational mechanisms and seven potential transformational mechanisms that can explain SHPI outcomes were identified from 28 articles. The results were integrated into a framework to pinpoint elements that facilitate or impede intersectoral SHPI implementation. Conclusion: The results of this synthesis support a more comprehensive approach to evaluating SHPI, and improved consideration of intersectoral collaboration and the complexity associated with this type of intervention.