Abstract Background Social capital has been found to be positively associated with various health and well-being outcomes amongst children. Less is known about how social capital may be generated and specifically in relation to children in the school setting. Drawing on the social cohesion approach and the democratic health educational methodology IVAC (Investigation – Vision – Action – Change) the aim of this study was to examine the effect of the Health Promoting School intervention ‘We Act – Together for Health’ on children’s cognitive social capital. Method A quasi-experimental controlled pre- and post-intervention study design was conducted with 548 participants (mean age 11.7 years). Cognitive social capital was measured as: horizontal social capital (trust and support in pupils); vertical social capital (trust and support in teachers); and a sense of belonging in the school using questions derived from the Health Behaviour in School Children study. A series of multilevel ordinal logistic regression analyses was performed for each outcome to estimate the effect of the intervention. Result The analyses showed no overall significant effect from the intervention on horizontal social capital or vertical social capital at the six-month follow-up. A negative effect was found on the sense of belonging in the school. Gender and grade appeared to be important for horizontal social capital, while grade was important for sense of belonging in the school. The results are discussed in relation to We Act’s implementation process, our conceptual framework and methodological issues and can be used to direct future research in the field. Conclusion The study finds that child participation in health education can affect the children’s sense of belonging in the school, though without sufficient management support, this may have a negative effect. With low implementation fidelity regarding the Action and Change dimension of the intervention at both the school and class level, and with measurement issues regarding the concept of social capital, more research is needed to establish a firm conclusion on the importance of the children’s active participation as a source for cognitive social capital creation in the school setting. Trial registration https://www.isrctn.com/ISRCTN85203017