We piloted an intervention that placed a people-centred health systems governance approach in the hands of multi-stakeholder committees that govern provincial and district health systems in Afghanistan. We report the results of this intervention from three provinces and eleven districts in Afghanistan over a six month period. This mixed-methods exploratory case study uses analysis of governance self-assessment scores, health management information system data on health system performance, and focus group discussions. The outcomes of interest are governance scores and health system performance indicators. We document the application of a people-centred health systems governance conceptual model based on applying four effective governing practices: cultivating accountability, engaging with stakeholders, setting a shared strategic direction, and stewarding resources responsibly. We found that health systems governance can be improved in fragile and conflict affected environments, and that consistent application of the effective governing practices is key to improving governance. Intervention was associated with a 20% increase in antenatal care visit rate in pilot provinces.