The need for evidence-based practice calls for research focussing not only on the effectiveness of interventions and their translation into policies, but also on implementation processes and the factors influencing them, in particular for complex health system policies. In this paper, we use the lens of one of the health system's 'building blocks', human resources for health (HRH), to examine the implementation of official policies on HRH incentives and the emergence of informal practices in three districts of Sierra Leone. Our mixed-methods research draws mostly from 18 key informant interviews at district level. Data are organised using a political economy framework which focuses on the dynamic interactions between structure (context, historical legacies, institutions) and agency (actors, agendas, power relations) to show how these elements affect the HRH incentive practices in each district. It appears that the official policies are re-shaped both by implementation challenges and by informal practices emerging at local level as the result of the district-level dynamics and negotiations between District Health Management Teams (DHMTs) and nongovernmental organisations (NGOs). Emerging informal practices take the form of selective supervision, salary supplementations and per diems paid to health workers, and aim to ensure a better fit between the actors' agendas and the incentive package. Importantly, the negotiations which shape such practices are characterised by a substantial asymmetry of power between DHMTs and NGOs. In conclusion, our findings reveal the influence of NGOs on the HRH incentive package and highlight the need to empower DHMTs to limit the discrepancy between policies defined at central level and practices in the districts, and to reduce inequalities in health worker remuneration across districts. For Sierra Leone, these findings are now more relevant than ever as new players enter the stage at district level, as part of the Ebola response and post-Ebola reconstruction.