Coverage of COVID-19 vaccines in Somalia remains low, including among health workers. This study aimed to identify factors associated with COVID-19 vaccine hesitancy among health workers. In this cross-sectional, questionnaire-based study, 1476 health workers in government and private health facilities in Somalia's federal member states were interviewed face-to-face about their perceptions of and attitudes toward COVID-19 vaccines. Both vaccinated and unvaccinated health workers were included. Factors associated with vaccine hesitancy were evaluated in a multivariable logistic regression analysis. Participants were evenly distributed by sex, and their mean age was 34 (standard deviation 11.8) years. The overall prevalence of vaccine hesitancy was 38.2%. Of the 564 unvaccinated participants, 39.0% remained hesitant. The factors associated with vaccine hesitancy were: being a primary health care worker (adjusted odds ratio (aOR) = 2.37, 95% confidence interval (CI): 1.15-4.90) or a nurse (aOR = 2.12, 95% CI: 1.05-4.25); having a master's degree (aOR = 5.32, 95% CI: 1.28-22.23); living in Hirshabelle State (aOR = 3.23, 95% CI: 1.68-6.20); not having had COVID-19 (aOR = 1.96, 95% CI: 1.15-3.32); and having received no training on COVID-19 (aOR = 1.54, 95% CI: 1.02-2.32). Despite the availability of COVID-19 vaccines in Somalia, a large proportion of unvaccinated health workers remain hesitant about being vaccinated, potentially influencing the public's willingness to take the vaccine. This study provides vital information to inform future vaccination strategies to achieve optimal coverage.