ObjectiveTo verify the effects of replacing exercises targeted on core/hip muscles by exercises targeted on leg/foot muscles in a rehabilitation program for patellofemoral pain (PFP). DesignRandomized Controlled Trial. ParticipantsFifty women with PFP. MethodsPFP participants were randomized into the standard rehabilitation group (SRG, n = 25) or distal exercise group (DEG, n = 25). Knee pain, patient-reported function, dynamic knee valgus and muscle strength were measured at baseline and after six and twelve weeks of the program start. ResultsSRG and DEG presented similar responses to rehabilitation (except for muscle strengthening). Knee pain reduced after 6 weeks (SRG: −37.7%, ES = 1.23; DEG: −30%, ES = 0.93) and 12 weeks (SRG: −47.4%, ES = 1.53; DEG: −43.3%, ES = 1.46). Patient-reported function improved after 6 weeks (SRG: +7.3%, ES = 0.45; DEG: +3.8%, ES = 0.22) and 12 weeks (SRG: +14.1%, ES = 0.80; DEG: +8.8%, ES = 0.50). Dynamic knee valgus reduced after 12 weeks (SRG: −29.7%, ES = 0.38; DEG: −34.5%, ES = 0.32). Both groups experienced increases in knee extension strength (SRG: +9%, ES = 0.28; DEG: +6%, ES = −0.29), but only SRG had strength gains for hip abduction (+10%, ES = 0.36) and extension (+11%, ES = 0.44). ConclusionExercises targeted on core/hip muscles can be replaced by exercises targeted on leg/foot muscles in a lower limb exercise-based rehabilitation program for women with PFP. Clinical trial registrationNCT03663595.