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To investigate the effects of an exhaustive run on trunk and lower extremity strength and mechanics in patients with and without patellofemoral pain (PFP), we hypothesized that strength would decrease and mechanics would change after the exhaustive run.Nineteen subjects with PFP and 19 controls participated (10 men and 9 women per group). Lower extremity and trunk mechanics during running, body mass–normalized strength, and pain assessments before and after an exhaustive run were quantified. A repeated-measures ANOVA was used to assess group differences and exhaustion-related changes (P < 0.05), with t-test post hoc analyses performed when significant interactions were identified (P < 0.0125).Pain significantly increased with the exhaustive run in the PFP group (P = 0.021). Hip strength was reduced after the exhaustive run, more so in those with PFP (abduction: before = 0.384 ± 0.08, after = 0.314 ± 0.08, P < 0.001; external rotation: before = 0.113 ± 0.02, after = 0.090 ± 0.02, P < 0.001). Persons with PFP also demonstrated increased knee flexion (before = 41.6° ± 5.5°, after = 46.9° ± 7.5°, P < 0.001), hip flexion (before = 30.4° ± 6.8°, after = 42.5° ± 9.7°, P < 0.001), and anterior pelvic tilt (before = 7.2° ± 5.1°, after = 13.3° ± 6.7°, P = 0.001) after the exhaustive run compared to controls. Trunk flexion increased in both PFP (before = 13.09° ± 6.2°, after = 16.31° ± 5.3°, P < 0.001) and control (before = 1393° ± 4.7°, after = 15.99° ± 5.9°, P < 0.001) groups. Hip extension (before = −2.09 ± 0.49 N·m·kg−1, after = −2.49 ± 0.54 N·m·kg−1, P = 0.002) moments increased only in subjects with PFP.Exhaustive running results in reduced hip strength in subjects with PFP; however, this did not result in changes to hip internal rotation or adduction kinematics. Kinematic and kinetic changes after the exhaustive run are more indicative of compensatory changes to reduce pain. Increasing trunk flexion during running might provide pain relief during running; however, reducing anterior pelvic tilt may also warrant attention during treatment.