One hundred and ninety nine patients with patellofemoral pain (PFP) were randomized to undergo a HIP protocol (n=111) or a KNEE rehabilitation protocol (n=88) for 6 weeks. The primary outcomes of interest were pain evaluated using the Visual Analogue Scale (VAS) and function measured using the Anterior Knee Pain Scale (AKPS). Secondary outcomes of interest included the muscle strength (i.e., maximum voluntary isometric contraction of the hip abductors, hip extensors, hip external rotators, hip internal rotators, and knee extensors) and core endurance (i.e., anterior, posterior, and lateral muscles). Primary outcomes were measured at 1, 2, 3, 4, 5, and 6-weeks follow-up. Secondary outcomes were measured at 6-weeks follow-up only. Moreover, compliance was also evaluated. Results demonstrated that pain using VAS and function were statistically significantly improved from baseline in both groups. For VAS pain, significant improvement was observed in the HIP group starting at 3 weeks follow-up, and at 4 weeks in the HIP group, both continuing until week 6 (p≤0.05). For AKPS scores, both groups were statistically significantly reduced compared to baseline at 2-weeks continuing until 6 weeks follow-up (p≤0.05). In the percent change from baseline in maximum voluntary isometric force measures for both hip abductor and extensor muscles, the HIP protocol statistically significantly improved scores compared to the KNEE protocol (p≤0.05). However, the maximum voluntary isometric force for hip extensor rotators, hip internal rotators, and knee extensors were statistically significantly improved in both groups at 6-weeks when compared to the baseline (p≤0.05). For the core endurance outcomes, only posterior muscles were statistically significantly improved at 6-weeks follow-up compared to baseline in the HIP group, but this was not observed in the KNEE group. In addition, the HIP protocol had a compliance rate of 80.3% whereas the KNEE protocol had a compliance rate of 81.7%.