BackgroundTo determine the effects of negative heel shoes on perceived pain and knee biomechanical characteristics of runners with patellofemoral pain (PFP) during running.MethodsSixteen runners with PFP ran in negative (−11 mm drops) and positive (5 mm drops) heel shoes while visual analog scale (VAS) scores, retroreflective markers, and ground reaction force were acquired by applying a 10‐cm VAS, infrared motion capture system, and a three‐dimensional force plate. Knee moment, patellofemoral joint stress (PFJS), and other biomechanical parameters during the stance phase were calculated based on inverse dynamics and a biomechanical model of the patellofemoral joint.ResultsThe foot inclination angle, peak PFJS during the stance phase, patellofemoral joint reaction force, knee extension moment, and quadriceps force at the time of peak PFJS of runners with PFP in negative heel shoes were lower than that in positive heel shoes, no significant difference was found in VAS scores, knee flexion angle, patellofemoral contact area, and quadriceps moment arm at the time of peak PFJS.ConclusionsCompared to positive heel shoes, running in negative heel shoes decreases peak PFJS in runners with PFP, which may decrease patellofemoral joint loading, thus reducing the possibility of further development of PFP.Trail RegistrationSports Science Experiment Ethics Committee of Beijing Sport University. 2023095H, April 18, 2023 (prospectively registered).