Anterior knee pain (AKP) is a common pathological condition, particularly among young people and athletes, associated to an abnormal motion of the patella during the bending of the knee and possibly dependent on a muscular or structural imbalance. A lack of synergy in the quadriceps muscles results in a dynamic misalignment of the patella, which in turn produces pain. AKP rehabilitative therapy consists of conservative treatment whose main objective is to strengthen the Vastus Medialis. The aim of this article is to study the quadriceps muscle control strategy in AKP patients during an isokinetic exercise. Analysis of the muscle activation strategy is important for an objective measurement of the knee functionality in that it helps to diagnose and monitor the rehabilitative treatment. Surface electromyography (EMG) from the three superficial muscles of the femoral quadriceps during a concentric isokinetic exercise has been analyzed along with the signals of knee joint position and torque. A group of 12 AKP patients has been compared with a group of 30 normal subjects. Analysis of the grand ensemble average of the EMG linear envelopes in AKP patients reveals significant modifications in Vastus Medialis activity compared to the other quadriceps muscles. In order to study the synergy of the muscles, temporal identifiers have been associated to the EMG linear envelopes. To this end, EMG linear envelope decomposition in Gaussian pulses turned out to be effective and the results highlight an appreciable delay in the activation of the Vastus Medialis in AKP patients. This muscular unbalance can explain the abnormal motion of the patella.