Vaccination attitudes among healthcare workers (HCWs) predict their level of vaccination uptake and intention to recommend vaccinations to their patients. To our knowledge, no study has been conducted in South Africa to assess hesitancy toward influenza vaccines among HCWs. We adapted a questionnaire developed and validated by Betsch and colleagues and used it to conduct online and face-to-face interviews among HCWs at the start of the COVID-19 vaccine rollout. Multivariate logistic regression was used to assess predictors of influenza vaccine hesitancy. Of 401 participants, 64.5% were women, 49.2% were nurses, and 12.5% were physicians. A total of 54.9% were willing to accept, 20.4% were undecided, and 24.7% intended to refuse influenza vaccination. Participants who were above 25 years of age and physicians were more likely to accept the vaccine. Key predictors of vaccine acceptance were confidence in the effectiveness, consideration of benefits and risks, and willingness to be vaccinated to protect others. Influenza vaccine hesitancy was highest in those who did not trust that influenza vaccines are safe. For future flu seasons, tailored education programs on the safety and effectiveness of flu vaccines targeting younger HCWs, could be vital to improving vaccine uptake.