While vaccination is the only established option to prevent a susceptible host from influenza, we have yet to clarify the decision-making mechanisms of vaccine uptake among Japanese university and college students. We aimed to explore vaccination coverage and the related demographic, sociocultural, and socioeconomic factors among university students. We performed a cross-sectional survey involving 604 students at Hokkaido University. Participants were asked if they received influenza vaccination in advance of the 2018/19 season, and subsequently, their demographic and sociocultural/socioeconomic characteristics were surveyed. We also explored the mechanisms underlying students’ vaccination decisions. Vaccination coverage was estimated at 27.3% (95% confidence interval: 23.7–30.9). Freshmen (p < 0.0001) were significantly associated with choosing vaccination, and their odds ratio of vaccination was 11.3 (95% confidence interval: 6.2–20.7) times greater than students in other years. Among students other than freshmen, students belonging to medicine- and healthcare-related faculties were vaccinated three times more frequently than other students, and the coverage in students from Hokkaido was twice as large as that for students from other prefectures. Moreover, extracurricular activity was a positive predictor of vaccination. Although the coverage was as small as 27.3% among university students, freshmen in Japan have high vaccination coverage, which we believe is associated with the entrance examination during high influenza activity. In addition to exposing students to proper education regarding their risk self-assessment, consciousness raising via appropriate understanding of influenza and its severity and offering vaccination at university health centers at a reasonable cost may promote vaccine acceptance.