Background Although there is widespread agreement that strong district manager decision-making improves health systems, understanding about how the design and implementation of capacity-strengthening interventions work is limited. The Ghana Health Service has adopted the Leadership Development Programme (LDP) as one intervention to support the development of management and leadership within district teams. This paper seeks to address how and why the LDP ‘works’ when it is introduced into a district health system in Ghana, and whether or not it supports systems thinking in district teams. Methods We undertook a realist evaluation to investigate the outcomes, contexts, and mechanisms of the intervention. Building on two working hypotheses developed from our earlier work, we developed an explanatory case study of one rural district in the Greater Accra Region of Ghana. Data collection included participant observation, document review, and semi-structured interviews with district managers prior to, during, and after the intervention. Working backwards from an in-depth analysis of the context and observed short- and medium-term outcomes, we drew a causal loop diagram to explain interactions between contexts, outcomes, and mechanisms. Results The LDP was a valuable experience for district managers and teams were able to attain short-term outcomes because the novel approach supported teamwork, initiative-building, and improved prioritisation. However, the LDP was not institutionalised in district teams and did not lead to increased systems thinking. This was related to the context of high uncertainty within the district, and hierarchical authority of the system, which triggered the LDP’s underlying goal of organisational control. Conclusions Consideration of organisational context is important when trying to sustain complex interventions, as it seems to influence the gap between short- and medium-term outcomes. More explicit focus on systems thinking principles that enable district managers to better cope with their contexts may strengthen the institutionalisation of the LDP in the future.