Introduction Health technology assessment (HTA) is an area that remains less implemented in low- and lower middle-income countries. The aim of the study is to understand the perceptions of stakeholders in Uganda towards HTA and its role in decision making, in order to inform its potential implementation in the country. Methods The study takes a cross-sectional mixed methods approach, utilising an adapted version of an International Decision Support Initiative questionnaire with both semi-structured and open-ended questions. We interviewed thirty key informants from different stakeholder institutions in Uganda that have decision making roles in the health sector. Results All participants perceived HTA as an important tool for decision making. Allocative efficiency was regarded as the most important use of HTA receiving the highest average score (8.8 out of 10), followed by quality of healthcare (7.8/10), transparency (7.6/10), budget control (7.5/10) and equity (6.5/10). There was concern that some of the uses of HTA may not be achieved in reality if there was political interference during the HTA process. The technology areas that interviewees highlighted as needing HTA type evaluations urgently were identified as medicines (60.0% of the participants), diagnostics (53.3%), vaccines (40.0%), and public health programs (26.7%). The study participants identified development partners as the most likely potential users of HTA (66.7% of participants), followed by Ministry of Health (43.3%). Conclusion Interviewed stakeholders in Uganda viewed the role of HTA positively, suggesting that there exists a promising environment for the establishment and operationalisation of HTA as a tool for decision making within the health sector. However, sustainable development and application of HTA in Uganda will require adequate capacity both to undertake HTAs and to support their use and uptake.