Recently, there has been attention to the clinical application of closed kinetic chain and joint isolation exercise. Our purpose was to compare the effect of joint isolation and closed kinetic chain exercise on quadriceps muscle performance and perceived function in patients with patellofemoral pain. Twenty-three patients participated in an 8-week training period and were assigned to either a closed kinetic chain or a joint isolation exercise training group. An 8-inch (20.3 cm) retro step-up test was performed at baseline, 8 weeks, and 1 year. Seated knee extension testing was measured at baseline and at 8 weeks using peak concentric torque on an isokinetic dynamometer at 90 degrees/sec, 180 degrees/sec, and 360 degrees/sec. Perceived functional status was rated as excellent, good, fair, or poor based on questionnaire response. Statistical analysis showed that both groups had significant improvement in peak torque at all speeds, but only the closed kinetic chain group showed significant improvement in closed kinetic chain testing and perceived functional status. We concluded that closed kinetic chain training may be more effective than joint isolation exercise in restoring function in patients with patellofemoral dysfunction.