This study aimed to assess the perception of COVID-19 risk and the adherence to protective measures among medical students after vaccination. We conducted a cross-sectional survey on a convenience sample of students from all the 18 governmental medical schools in Egypt. A total of 2273 students participated in the online self-administered questionnaire. Around 8 in 10 (83.2%) students were fully vaccinated, of which 17.9% received the booster dose. Only 36.9% believed that COVID-19 is serious on the individual level. The majority (73.9%) strongly or slightly agreed they may become infected after vaccination if they do not follow the preventive measures. We observed a slow decline in the perceived risk of vulnerability and susceptibility to COVID-19 infection among students in parallel to a growing perception of self-efficacy and controllability. Less than one-third (28.9%) of students showed good adherence to protective measures. However, this was lower than the previously reported adherence in the same population before vaccination. Female students, those in the first academic year, those who did not contract COVID-19 infection before, and those with a higher perception of susceptibility and perceived controllability were more likely to perform better at protective measures.