The purpose of this study was to compare the effectiveness of non-operative and post-operative physiotherapy-rehabilitation programmes in patellofemoral pain syndrome that originated from patellofemoral malalignment. Forty-two subjects (21 non-operative, 21 postoperative) were included in the study. Pain, patellar tilt, congruence, sulcus and Q angles, Cincinnati scale, functional tests, hamstring tightness, iliotibial band tightness, and thigh circumference measurement were compared. When the pre-treatment data were compared within groups, there were statistically significant differences in favour of post-operative group as regards pain, hamstring tightness and Q angle (p < 0.05). When the post-treatment data were compared within both groups, there were significant differences in favour of postoperative group as regards pain, patellar tilt congruence angles, vertical jump tests, standing broad jump, and squat tests (p < 0.05).