BackgroundVaccines play a crucial role in eradicating and containing disease outbreaks. Therefore, understanding the reasons behind vaccine refusal and associated factors is essential for improving vaccine acceptance rates. Our objective was to examine the determinants of COVID-19 vaccine non-uptake and explore the reasons for non-uptake among healthcare workers (HCWs) in Uganda.MethodsBetween July and August 2021, we conducted a cross-sectional study among healthcare workers in primary healthcare facilities (private and government) in Entebbe Municipality, Uganda. Participants were recruited using convenience sampling, and consenting individuals received credentials to access an electronic database and complete a structured questionnaire. There were no established HCWs contact registers in the municipality, and the study was conducted during a national lock down, therefore, the HCWs who were on duty at the time of the study were approached. The survey questions were based on the ‘3Cs’ model of vaccine hesitancy and focused on confidence, convenience, and complacency factors. Non-uptake of vaccines was defined as not having received any of the available vaccines in the country. We employed counts, percentages, and simple logit models to summarize the reasons for non-uptake of COVID-19 vaccines and to identify associated factors.ResultsThe study recruited 360 HCWs, 61.7% of whom were female, with an average age of 31 years (SD = 7.9). Among them, 124 (34.4%) healthcare workers did not receive any COVID-19 vaccine. Non-uptake of COVID-19 vaccines was independently associated with several factors, including age [35 + years adjusted odds ratio (aOR) = 0.30, 95% CI: 0.13–0.66 compared with 18–24 years], facility ownership [government, aOR = 0.22 (0.10–0.49) compared with private not-for-profit], previous testing for coronavirus [yes, aOR = 0.35 (0.19–0.65)], and previous involvement in COVID-19 vaccine activities [yes, aOR = 0.17 (0.10–0.29)]. The primary reasons cited for non-uptake of COVID-19 vaccines were related to a lack of confidence in the vaccines, such as concerns about side effects (79.8%) and the need for more time to understand the vaccines (89.5%), as well as the importance of weighing benefits and risks (84.7%) before being vaccinated. A smaller proportion, approximately 23%, cited reasons related to complacency and lack of convenience in accessing vaccination services.ConclusionThe high proportion of non-uptake of COVID-19 vaccines among this population primarily stems from a lack of confidence and trust in the vaccines, coupled with insufficient time allowed for users to make informed decisions. This underscores the urgent need for ongoing monitoring and trend analysis of vaccine non-uptake to guide the development and implementation of strategies aimed at building and sustaining vaccine confidence. Adequate time should be allowed to explain benefits of vaccination to the population to allay fears that might exist before actual vaccination is rolled out.