BackgroundIn a decentralised health system, district health managers are tasked with planning for health service delivery, which should be evidence based. However, planning in low-income countries such as Uganda has been described as ad hoc. A systematic approach to the planning process using district-specific evidence was introduced to district health managers in Uganda. However, little is known about how the use of district-specific evidence informs the planning process. In this study, we investigate how the use of this evidence affects decision-making in the planning process and how stakeholders in the planning process perceived the use of evidence.MethodsA convergent parallel mixed-methods study design was used, where quantitative data was collected from district health annual work plans for the financial years 2012/2013, 2013/2014, 2014/2015 and 2015/2016 as well as from bottleneck analysis reports for 2012, 2013, 2014 and 2015. Qualitative data was collected through semi-structured interviews with key informants from the two study districts.ResultsDistrict managers reported that they were able to produce more robust district annual work plans when they used the systematic approach of using district-specific evidence. Approximately half of the prioritised activities in the annual work plans were evidence based. Procurement and logistics, training, and support supervision activities were the most prioritised activities. Between 4% and 5.5% of the total planned expenditure was for child survival, of which 47% to 94% was from donor and other partner contributions.ConclusionDistrict-specific evidence and a structured process for its use to prioritise activities and make decisions in the planning process at the district level helped systematise the planning process. However, the reported limited decision and fiscal space, inadequate funding and high dependency on donor funding did not always allow for the use of district-specific evidence in the planning process.