Background: Patellofemoral pain (PFP) is a common knee pain condition where hip and knee exercises help improve treatment outcomes. This study compared the acute effect of hip versus knee exercises on anti-nociceptive and pro-nociceptive mechanisms in young females with long-standing PFP. Methods: In this randomized cross-over study, 29 females with PFP performed hip and knee exercises in randomized order during a single day. Pressure pain thresholds (PPTs) were assessed by handheld pressure algometry at the patella, the tibialis anterior muscle, and the contralateral elbow. Cuff pressure algometry at the lower legs was used to assess pain detection threshold (cPDT) and tolerance (cPTT) as well as conditioned pain modulation (CPM: change in cPDT during contralateral cuff pain conditioning) and temporal summation of pain (TSP: ten painful cuff stimulations assessed on a visual analogue scale [VAS]). Results: PPTs at the tibialis anterior muscle but not at the patella increased compared with baseline following both exercises (p <.002). Compared with baseline, the cPDTs and cPTTs increased after both types of exercises (p <.001). The cPTTs increased more after knee compared to hip exercises (p <.007). VAS scores for TSP were increased following hip exercises (p <.001) although the rate of VAS increase over repeated stimulations was not significantly affected by exercises. The CPM-effect was reduced after both types of exercises (p <.001). Conclusion: A general hypoalgesic response to slowly increasing pressure stimuli was observed following both hip and knee exercises as well as decreased conditioned pain modulation, potentially indicating an attenuated ability from exercise to inhibit pain.