High coverage of COVID-19 vaccination is claimed to be the most effective intervention to prevent the transmission of coronavirus disease. This study aimed to analyze the factors associated with willingness to accept COVID-19 vaccination among students of the Universitas Pattimura, Ambon, Indonesia. This cross-sectional study collected information using an online questionnaire distributed to students at Universitas Pattimura in January 2021, when the COVID-19 vaccination program was initiated in Indonesia. Guided by the Health Belief Model, potential predictors in this analysis were categorized as follows: (1) sociodemographic characteristics; (2) predisposing factors; (3) perceived susceptibility; (4) perceived benefits; and (5) perceived barriers. Data were analyzed using multivariate logistic regression analysis. We found that only 42.1% of the students were willing to receive the COVID-19 vaccine. The odds of students’ willingness to receive COVID-19 vaccination decreased by 52% in students who did not perceive themselves to be at risk of contracting COVID-19 (adjusted odds ratio [aOR]=0.48, 95% confidence interval [CI]: 0.34–0.68). The odds also decreased by 97% in those who strongly disagreed that the COVID-19 vaccine was safe and effective (aOR=0.03, 95% CI: 0.01–0.08), and by 45% in those who were neutral towards the statement if COVID-19 vaccination is the solution to end the pandemic (aOR=0.55, 95% CI: 0.36–0.84). However, the odds of willingness to receive COVID-19 vaccination increased by 53% in students showing neutrality toward fear of needles (aOR=1.53, 95% CI: 1.04–2.25). The odds of willingness to receive COVID-19 vaccination in students who were neutral towards the side effects of vaccination were >3 times higher than those who were concerned about the side effects of vaccination (aOR=4.05, 95% CI: 2.61–6.26). Health promotion strategies should be accompanied by efforts to reduce the harmful effects of rumors that may hinder students’ willingness to participate in COVID-19 vaccination programs.