This study compared the willingness to receive human papillomavirus (HPV) vaccination and the influencing factors between male and female university students who had never been vaccinated against HPV in China. University students were recruited from seven universities in China. A self‐administered questionnaire was used to collect information about demographic characteristics, willingness to HPV vaccination, and possible influencing factors including demographics, knowledge, and attitude toward HPV vaccination. The χ2 test was used to test the difference between males and females' knowledge and attitudes to HPV vaccination. Multivariate logistic regression was employed to detect the factors associated with willingness to HPV vaccination. A total of 7335 university students participated in the survey (3570 males and 3765 females). Over 70% of the participants had previously received sex education and knowledge. The average age of sexual debut was 17.5 years old. More male students reported acceptance of premarital sex than female students did (χ2 = 708.458, p < 0.001). Female students had better knowledge and attitudes to HPV in general, while male students perceived a higher chance of being infected by HPV compared with female students (χ2 = 6.047, p = 0.014). The level of knowledge (male: adjusted odds ratio [AOR] = 1.935, 95% confidence interval [CI]:1.516–2.470; female: AOR = 1.227, 95% CI: 1.055–1.428) and receiving sex education (male: AOR = 1.414, 95% CI: 1.109–1.804; female: AOR = 1.289, 95% CI: 1.064–1.562) were indicators of the HPV vaccination willingness for both genders. For male students, those who had ever inoculated optional self‐paid vaccines were more likely to receive the HPV vaccine than those who had not (AOR = 1.567, 95% CI: 1.242–1.977). Female students were more willing to be vaccinated against HPV, if they had higher living expenses (AOR = 1.395 and 3.717, 95% CI: 1.071–1.426 and 1.776–7.752), relatives or friends had certain cancer (AOR = 1.290, 95% CI: 1.095–1.518), ever had sexual experiences (AOR = 2.628, 95% CI: 1.788–3.863), and had ever consulted on HPV vaccination issues (AOR = 1.612, 95% CI: 1.367–1.901). In China, more active education should be provided to improve university students' knowledge and attitudes on HPV and HPV vaccination. Including HPV vaccine uptake for both males and females at recommended ages in National Immunization Program would be the most cost‐effective way to prevent HPV infection.