Patellofemoral pain (PFP) is a chronic condition that presents with patellar pain during various daily and recreational activities. Individuals with PFP have a wide range of impairments that result in long-term disability and reduced quality of life. Current interventions target hip muscle weakness with strength-based exercises, but recurrence rates are as high as 90%. A single feasibility study demonstrated success with power-based exercises; however, there is limited evidence evaluating pain or self-reported function in larger cohorts, and no study has assessed recurrence rates. This protocol details a study evaluating a strength-based rehabilitation programme compared with a strength-based programme incorporating power-based exercises in individuals with PFP. This single-blinded randomised controlled trial will evaluate 88 participants with PFP, aged 18-40 years old. Participants will be recruited from three universities, the surrounding community and sports medicine clinics. Participants will receive three telemedicine rehabilitation sessions a week for 6 weeks. The rehabilitation programme will consist of either strength-based exercises or a combination of power and strength-based exercises. Pain, subjective function and recurrence rates will be assessed at baseline, immediately after the intervention and at four follow-up time points: 6-month, 12-month, 18-month and 24-month postintervention. We will also assess neuromuscular function of the hips and global rating of change at each postintervention time point. Trial registration number NCT05403944.