Patellofemoral pain (PFP) is one of the most prevalent injuries in runners. Unfortunately, a substantial part of injured athletes do not recover fully from PFP in the long-term. Although previous studies have shown positive effects of gait retraining in this condition, retraining protocols often lack clinical applicability because they are time-consuming, costly for patients and require a treadmill. The primary objective of this study will be to compare the effects of two different two-week partially supervised gait retraining programs, with a control intervention; on pain, function and lower limb kinematics of runners with PFP. It will be a single-blind randomized clinical trial with six-month follow-up. The study will be composed of three groups: a group focusing on impact (group A), a group focusing on cadence (group B), and a control group that will not perform any intervention (group C). The primary outcome measure will be pain assessed using the Visual Analog Pain scale during running. Secondary outcomes will include pain during daily activities (usual), symptoms assessed using the Patellofemoral Disorders Scale and lower limb running kinematics in the frontal (contralateral pelvic drop; hip adduction) and sagittal planes (foot inclination; tibia inclination; ankle dorsiflexion; knee flexion) assessed using the MyoResearch 3.14—MyoVideo (Noraxon U.S.A. Inc.). The study outcomes will be evaluated before (t0), immediately after (t2), and six months (t24) after starting the protocol. Our hypothesis is that both partially supervised gait retraining programs will be more effective in reducing pain, improving symptoms, and modifying lower limb kinematics during running compared with the control group, and that the positive effects from these programs will persist for six months. Also, we believe that one gait retraining group will not be superior to the other. Results from this study will help improve care in runners with PFP, while maximizing clinical applicability as well as time and cost-effectiveness.