Objective To determine the acute effects of heel-to-toe drops of running shoes on the loading of the patellofemoral joint and Achilles tendon (AT) in runners with patellofemoral pain (PFP) during running. Methods Sixteen runners with PFP completed a running test while wearing running shoes with different heel-to-toe drop values. The retroreflective markers and ground reaction force were measured using an infrared motion capture system and a three-dimensional force plate. The patellofemoral joint stress (PFJS) and AT force were calculated based on biomechanical models of the patellofemoral joint and AT. Results When runners with PFP ran in negative heel shoes, the PFJS (P<0.001) during 39%–47% of the stance phase, maximum PFJS, and cumulative PFJS (P<0.05) during the stance phase were lower than those in positive heel shoes. Meanwhile, the AT force (P<0.001) and cumulative AT force (P=0.001) during 12%–46% of the stance phase were larger than those in positive heel shoes. The AT force (P<0.001) and cumulative AT force (P=0.023) in the negative-heel shoes during 12%–31% of the stance phase were higher than those in the zero-heel shoes. Conclusions Compared with runners with positive-heel shoes, runners with PFP running in negative-heel shoes had decreased PFJS and cumulative PFJS. This may potentially reduce the risk of further development of PFP. However, compared with zero- and positive-heel shoes, running in negative-heel shoes increases the AT force and cumulative AT force. This may increase the risk of AT injury. Runners with PFP are recommended to undergo acclimatization before shifting to negative-heel shoes. This would limit further progression of PFP without increasing the risk of AT injury.