Background: There is a growing body of literature on evidence-informed priority setting. However, the literature on the use of evidence when setting healthcare priorities in low-income countries (LICs), tends to treat the healthcare system (HCS) as a single unit, despite the existence of multiple programs within the HCS, some of which are donor supported. Objectives: (i) To examine how Ugandan health policy-makers define and attribute value to the different types of evidence; (ii) Based on 6 health programs (HIV, maternal, newborn and child health [MNCH], vaccines, emergencies, health systems, and non- communicable diseases [NCDs]) to discuss the policy-makers’ reported access to and use of evidence in priority setting across the 6 health programs in Uganda; and (iii) To identify the challenges related to the access to and use of evidence. Methods: This was a qualitative study based on in-depth key informant interviews with 60 national level (working in 6 different health programs) and 27 sub-national (district) level policy-makers. Data were analysed used a modified thematic approach. Results: While all respondents recognized and endeavored to use evidence when setting healthcare priorities across the 6 programs and in the districts; more national level respondents tended to value quantitative evidence, while more district level respondents tended to value qualitative evidence from the community. Challenges to the use of evidence included access, quality, and competing values. Respondents from highly politicized and donor supported programs such as vaccines, HIV and maternal neonatal and child health were more likely to report that they had access to, and consistently used evidence in priority setting. Conclusion: This study highlighted differences in the perceptions, access to, and use of evidence in priority setting in the different programs within a single HCS. The strong infrastructure in place to support for the access to and use of evidence in the politicized and donor supported programs should be leveraged to support the availability and use of evidence in the relatively under-resourced programs. Further research could explore the impact of unequal availability of evidence on priority setting between health programs within the HCS.