Millions of people have died because of the COVID-19 pandemic. The vaccination campaign helped tackle the pandemic and saved millions of lives. In a retrospective pharmacovigilance study, we explored the safety of the BNT162b2 (Comirnaty) vaccine among healthcare workers (HCWs) in a large Italian teaching hospital, and 2428 Adverse Events Reports (AERs) filed by HCWs after the administration of the first dose of vaccine were collected and analyzed, reporting the results quantitively and comparing them to the vaccine Summary of Product Characteristics (SPC). Spearman’s correlation coefficients were computed to investigate the correlation among reported adverse effects, and recurrent clusters of symptoms were investigated through the Principal Component Analysis (PCA) and k-means Cluster Analysis. The BNT162b2 vaccine’s safety profile was favorable, with predominant reports of early onset, mild, non-serious and short-term resolved symptoms. We observed higher than the expected frequency for various non-serious undesirable effects, especially among those listed and classified as less common in the SPC. Furthermore, we identified three clusters of adverse effects that were frequently reported together, defined by the presence/absence of fatigue, malaise, localized pain, chills, pyrexia, insomnia, nausea and injection site pain. Post-marketing pharmacovigilance activities, together with targeted public health interventions, can be valuable tools to promote vaccination and improve the control of the spread of the pandemic, especially in sensitive settings and populations such as hospitals and healthcare professionals.