To explore whether collegiate recreational runners of different genders exhibit different lower extremity kinematics following a 5 km running time trial. Thirty collegiate recreational runners (15 males, 15 females) participated. The participants performed kinematic tests using IMUs before and after the 5 km running time trial. Spatiotemporal parameters were recorded via the Garmin HRM-RUN during the 5 km running time trial. The peak hip, knee and ankle joint angles and angular velocity were compared within and between groups using two-way analysis of variance. Spatiotemporal parameters were compared between groups using independent t tests. In terms of kinematic parameters, gender and time have a significant interaction effect on the peak knee internal rotation angle (P = 0.036) after 5 km running time trial. The peak ankle eversion angular velocity after running was significantly greater than that before running in male runners (P = 0.015). In terms of spatiotemporal parameters, the average cadence of females was significantly greater than that of males during running (P = 0.003). The Collegiate recreational runners presented gender-specific lower extremity kinematic characteristics following a 5 km running time trial. The peak knee internal rotation angle significantly increased after the 5 km running time trial in female runners. It should be paid more attention to the association between gender-specific lower extremity kinematic characteristics and running-related injuries in the future.