Healthcare workers were prioritized in vaccination campaigns globally because they are exposed to the highest risk of contamination by SARS-CoV-2. This study evaluated the self-reported post-vaccination side effects of inactivated (BBIBP-CorV and CoronaVac) and adenoviral vector-based (AZD1222, Gam-COVID-Vac and Ad26.COV2.S) vaccines among Algerian healthcare workers using a validated questionnaire. The final analysis included 721 healthcare workers, with a predominance of females (59.1%) and younger individuals 20–30 years old (39.4%). Less than half (49.1%) of the respondents reported at least one local side effect, while 53.8% reported at least one systemic side effect. These side effects were more prevalent among viral vector vaccinees than inactivated virus vaccinees. The most common local side effects were injection site pain (39%) and arm pain (25.4%), while fatigue (34.4%), fever (28.4%), headache (24.8%) and myalgia (22.7%) were the most prevalent systemic side effects. The side effects appeared earlier among inactivated virus vaccines recipients and generally lasted for 2 to 3 days for the two vaccinated groups. The risk factors associated with a higher prevalence of side effects included female gender, allergic individuals, individuals with regular medication, those who contracted the COVID-19 disease and those who received two doses for both inactivated and viral-based vaccines groups. Despite the higher prevalence of post-vaccination side effects among adenoviral vector vaccines recipients, both vaccines groups were equally effective in preventing symptomatic infections, and no life-threatening side effects were reported in either vaccine group.