Background Vaccination is one of the most successful public health interventions for preventing infectious diseases. A successful vaccination program depends on high coverage, and health care workers (HCWs) play a pivotal role in ensuring high uptake of vaccines in the population. COVID-19 vaccines have been proven to be efficacious, and vaccination campaigns have been ongoing, however there is a perceived high vaccine hesitancy even among health care workers in Uganda. This study aimed at describing the facilitators, barriers to and level of uptake of COVID 19 vaccines among healthcare workers in primary healthcare facilities in an urban setting in Uganda. Methods We conducted an online cross-sectional survey among healthcare workers in private and public healthcare facilities in Entebbe municipality between July 2021 and August 2021. Data was collected using an online questionnaire. Uptake of the vaccines among healthcare workers was analysed as proportions, and logistic regression was used to analyse barriers and facilitators to uptake of COVID 19 vaccines. Results The study enrolled 360 participants, with 61.7% (n=222) females. A total of 236 (65.6%) healthcare workers had received at least one dose of COVID 19 vaccine with higher uptake among females 64%(n=151). Age above 40 years (OR 4.29), participating in COVID 19 vaccine related activities (OR 4.18) and having had a negative SARS-COV-2 test result (OR 1.79) increased the odds of having been vaccinated. Working in either a private for profit (OR 0.23) or a private not for profit (OR 0.19) reduced the odds of having been vaccinated. History of having cared for a COVID 19 patient and having a positive SARS-COV-2 test result did not influence the uptake of the vaccines in the study population. Conclusion Vaccine uptake among healthcare workers was close to the World Health Organisation (WHO) recommended uptake of 70% by mid-2022.