This study investigated the intention to get the coronavirus disease of 2019 (COVID-19) vaccine and its associated factors among Japanese university students. A cross-sectional survey was conducted from March to May 2021 via an e-learning platform at Akita University. Participants were 1776 graduate and undergraduate students who answered the survey on vaccine intention, the health belief model (HBM), sociodemographic characteristics, and concerns over COVID-19-related situations. Vaccine intention was stratified into active, slightly less, and no intention, and the associated factors were determined using the multinomial logistic regression model. Results showed that 56.7% of students had active intention, followed by slightly less intention (34.5%) and no intention (8.8%). After adjusting for covariates, healthcare course, perceived severity (life-threatening and serious social consequences), and perceived benefits from HBM were significantly associated with active intention, with adjusted odds ratios of 4.02 (95% confidence interval [CI], 2.11–7.67), 1.40 (95% CI, 1.16–1.69), 1.23 (95% CI, 1.04–1.46), and 2.03 (95% CI, 1.66–2.49), respectively; perceived barriers (side effect, troublesome, and parent disagreement) were adversely associated with active intention. The public health strategy to improve students’ vaccine uptake requires providing accurate information on vaccine safety and efficacy while removing any barriers to vaccination.