Although there is evidence that non-government health system actors can individually or collectively develop practical strategies to address primary health care (PHC) challenges in the community, existing frameworks for analysing health system governance largely focus on the role of governments, and do not sufficiently account for the broad range of contribution to PHC governance. This is important because of the tendency for weak governments in low- and middle-income countries (LMICs). We present a multi-level governance framework for use as a thinking guide in analysing PHC governance in LMICs. This framework has previously been used to analyse the governance of common-pool resources such as community fisheries and irrigation systems. We apply the framework to PHC because, like common-pool resources, PHC facilities in LMICs tend to be commonly owned by the community such that individual and collective action is often required to avoid the 'tragedy of the commons'-destruction and degradation of the resource resulting from lack of concern for its continuous supply. In the multi-level framework, PHC governance is conceptualized at three levels, depending on who influences the supply and demand of PHC services in a community and how: operational governance (individuals and providers within the local health market), collective governance (community coalitions) and constitutional governance (governments at different levels and other distant but influential actors). Using the example of PHC governance in Nigeria, we illustrate how the multi-level governance framework offers a people-centred lens on the governance of PHC in LMICs, with a focus on relations among health system actors within and between levels of governance. We demonstrate the potential impact of health system actors functioning at different levels of governance on PHC delivery, and how governance failure at one level can be assuaged by governance at another level.