Females are two times more likely to develop patellofemoral pain (PFP) than males. Abnormal trunk and pelvis kinematics are thought to contribute to the pathomechanics of this condition. However, there is a scarcity of evidence investigating proximal segments kinematics in females with PFP. The purpose of this study was to investigate whether females with PFP demonstrate altered trunk, pelvis, and knee joint kinematics compared with healthy controls during running. Thirty-four females (17 PFP, 17 controls) underwent a 3-dimensional motion analysis during treadmill running at preferred and fixed speeds, each trial for 30 s. Variables of interest included magnitudes of peak angles for trunk (forward flexion, ipsilateral trunk lean), pelvis (anterior tilt, contralateral drop), knee (flexion, valgus, internal rotation), range of motion (RoM) of trunk and pelvis in sagittal and frontal planes and RoM of knee joint in the three cardinal planes of motion. Kinematic data were compared between groups using mixed model repeated measure analysis of variance with the trial as the repeated measure. The PFP group displayed significantly less pelvis frontal plane RoM, greater knee frontal plane RoM, and less knee sagittal plane RoM during running compared with controls, irrespective of running trial. No differences were found in peak kinematic variables between PFP and healthy groups. These results may suggest a rigid stabilization strategy at the pelvis, which the body has adapted to prevent further frontal plane knee malalignment. Less knee sagittal plane RoM may be indicative of another protective strategy in the PFP group to avoid patellofemoral joint reaction force. Clinical assessments and rehabilitative treatments may benefit from considering a global program with focus on pelvis kinematics in addition to the knee joint in females with PFP.