Vaccinations are a key prevention measure in fighting the COVID-19 pandemic. The BNT162b2 mRNA vaccine (BioNTech/Pfizer), the first to receive authorization, was widely used in the mass vaccination campaign in Italy. Healthcare workers were identified as a priority group for vaccination, but few studies have assessed its reactogenicity among the young working age population. An online survey was conducted to investigate the adverse reactions occurring in the 7 days following the first and second vaccination doses amongst resident doctors of the University of Genoa, employed at the IRCCS Ospedale Policlinico San Martino of Genoa, between 11 January and 16 March 2021. A total of 512 resident physicians were invited to participate in the study (female = 53.2%; mean age = 28.9 years), of whom 296 (female = 53.4%, mean age = 28.9 years) and 275 (female = 55.3%, mean age = 29.1 years) completed the survey after their first and second vaccination doses, respectively. In the 7 days following the first dose, most common adverse reactions were local pain (96.3%), fatigue (42.6%), headache (33.8%), arthromyalgia (28.0%), and 5.1% reported fever, while following the second dose, participants reported local pain (93.5%), fatigue (74.9%), headache (57.5%), arthromyalgia (58.2%), and fever (30.9%), with a higher prevalence among females. Systemic (but not local) reactions increased following the second vaccination, reaching severe intensity in 9.8% of participants and causing three or more events of moderate intensity in 23.7% of participants. Adverse reactions preventing regular daily activities could cause absenteeism among workers. These results can be useful to inform populations of young individuals, set expectations, and improve adherence to vaccination campaigns.