Females, as compared with males, have a higher proportion of injuries in the foot region. However, the reason for this gender difference regarding foot injuries remains unclear. This study aimed to investigate gender differences associated with rearfoot, midfoot, and forefoot kinematics during running. Twelve healthy males and 12 females ran on a treadmill. The running speed was set to speed which changes from walking to running. Three‐dimensional kinematics of rearfoot, midfoot, and forefoot were collected and compared between males and females. Furthermore, spatiotemporal parameters (speed, cadence, and step length) were measured. In the rearfoot angle, females showed a significantly greater peak value of plantarflexion and range of motion in the sagittal plane as compared with males (effect size (ES) = 1.55 and ES = 1.12, respectively). In the midfoot angle, females showed a significantly greater peak value of dorsiflexion and range of motion in the sagittal plane as compared with males (ES = 1.49 and ES = 1.71, respectively). The forefoot peak angles and ranges of motion were not significantly different between the genders in all three planes. A previous study suggested that a gender‐related difference in excessive motions of the lower extremities during running has been suggested as a contributing factor to running injuries. Therefore, the present investigation may provide insight into the reason for the high incidence of foot injuries in females.