ObjectivesData on the problem of physical activity-related injury (PARI) in university students and the risk factors for PARI among different genders are rare. We conducted a multicentre population-based study to investigate the occurrence of PARI and to explore the gender-specific risk factors for PARI among Chinese university students.DesignCross-sectional study.ParticipantsA total of 5341 students in grades 1–3 at eight universities in four Chinese cities were selected to complete the online questionnaires during March and April 2017. The questionnaires assessed sociodemographic characteristics, physical activity PA) involvement, sleep duration, sedentary behaviour and PARI experiences in the past 12 months.Main outcome measuresPARI during the past 12 months.ResultsAmong the 5341 participants, 1293 suffered from at least one PARI in the past 12 months, with an overall incidence rate of 24.2% (males: 26.2%, females: 23.2%) and an injury risk of 0.38 injuries/student/year (males: 0.48, females: 0.32). Over half of the injured (57.3%) experienced a withdrawal time of PA and nearly two-fifths (39.6%) required medical attention. Irrespective of gender, Shantou and Xi’an students, sports team members and those who engaged in sports and leisure-time vigorous-intensity PA (VPA) at a higher frequency were more likely to suffer from PARI. Male students who participated in sports and leisure-time VPA for long durations had a greater likelihood of sustaining PARI, while having a chronic condition and being involved in sports and leisure-time moderate-intensity PA at a higher frequency and longer duration were potential contributors to PARI among females.ConclusionsThe occurrence of PARI and its risk factors differed by gender, which provides a direction towards developing targeted and effective gender-specific preventative programmes to protect Chinese university students from PARI.