Patellofemoral pain is common amongst recreational runners and associated with altered running kinematics. However, it is currently unclear how sex may influence kinematic differences previously reported in runners with patellofemoral pain. This case-control study aimed to evaluate lower limb kinematics in males and females with and without patellofemoral pain during running. Lower limb 3D kinematics were assessed in 20 runners with patellofemoral pain (11 females, 9 males) and 20 asymptomatic runners (11 females, 9 males) during a 3 km treadmill run. Variables of interest included peak hip adduction, internal rotation and flexion angles; and peak knee flexion angle, given their previously reported association with patellofemoral pain. Age, height, mass, weekly run distance and step rate were not significantly different between groups. Mixed-sex runners with patellofemoral pain were found to run with a significantly greater peak hip adduction angle (mean difference = 4.9°, d = 0.91, 95% CI 1.4-8.2, p = 0.01) when compared to matched controls, but analyses for all other kinematic variables were non-significant. Females with patellofemoral pain ran with a significantly greater peak hip adduction angle compared to female controls (mean difference = 6.6°, p = 0.02, F = 3.41, 95% CI 0.4-12.8). Analyses for all other kinematic variables between groups (males and females with/without PFP) were non-significant. Differences in peak hip adduction between those with and without patellofemoral pain during running appear to be driven by females. This potentially highlights different kinematic treatment targets between males and females. Future research is encouraged to report lower limb kinematic variables in runners with patellofemoral pain separately for males and females.