Coordination across policy domains and government agencies is considered critical for addressing complex challenges such as inequities, urbanisation and climate change. However, the factors influencing coordination among government entities in low-income and middle-income countries are not well known and theory-based health policy and systems studies are limited. This paper examined the factors influencing coordination among government entities at the central government level in Uganda. Our findings suggest that achieving intragovernmental coordination requires more time and resources to guide the software aspects of institutional change—articulating a shared vision on coordination across government. Shaping incentives to align interests, managing coordination costs and navigating historical-institutional contexts are critical. Countervailing political actions and power dynamics should be judiciously navigated.