The aim of this study was to assess vaccination perception and the prevalence of the overall vaccination coverage (VC) and associated factors among university students. An online study was conducted among students of a university in Rouen (Normandy), France, in January 2021, with questions about the VC and perception of the vaccines. The convenience sample included 3089 students (response rate of 10.3%), with a mean age of 20.3 (SD = 1.9). The overall VC was 27.8% (39.2% for the healthcare students (HCS) and 21.3% for the non-HCS; p < 0.0001). Confidence (efficacy and security) was lower than the conviction of usefulness. The characteristics associated with VC were having the intention to be vaccinated against COVID-19, high perceptions of usefulness for their own health, having confidence in the vaccines’ efficacy and security, and a high estimated level of knowledge about vaccination. Education about the general interest and mechanism of action of vaccines could improve the perception of vaccines. Then, it is relevant to improve vaccination literacy and confidence in university students, who, as future adults and parents, will vaccinate themselves and their children; as well as healthcare students who are future healthcare workers and, therefore, will vaccinate and counsel their patients.