Since the 1990s, following similar reforms to its general politico-administrative systems, Uganda has decentralized its public healthcare system by shifting decision-making power away from its central Ministry of Health and towards more distal administrative levels. Previous research has used decision space—the decision-making autonomy demonstrated by entities in an administrative hierarchy—to measure overall health system decentralization. This study aimed to determine how the decision-making autonomy reported by managers of Ugandan healthcare facilities (de facto decision space) differs from that which they are allocated by official policies (de jure decision space). Additionally, it sought to determine associations between decision space and indicators of managerial performance. Using quantitative primary healthcare data from Ugandan healthcare facilities, our study determined the decision space expressed by facility managers and the performance of their facilities on measures of essential drug availability, quality improvement and performance management. We found managers reported greater facility-level autonomy than expected in disciplining staff compared with recruitment and promotion, suggesting that managerial functions that require less financial or logistical investment (i.e. discipline) may be more susceptible to differences in de jure and de facto decision space than those that necessitate greater investment (i.e. recruitment and promotion). Additionally, we found larger public health facilities expressed significantly greater facility-level autonomy in drug ordering compared with smaller facilities, which indicates ongoing changes in the Ugandan medical supply chain to a hybrid ‘push-pull’ system. Finally, we found increased decision space was significantly positively associated with some managerial performance indicators, such as essential drug availability, but not others, such as our performance management and quality improvement measures. We conclude that increasing managerial autonomy alone is not sufficient for improving overall health facility performance and that many factors, specific to individual managerial functions, mediate relationships between decision space and performance.