PURPOSE: To compare the effects of vastus medialis oblique (VMO) motor control retraining (MCR) and quadriceps strengthening (QS) exercises on the onset timing of the medial (VMO) and lateral (vastus lateralis, VL) quadriceps muscle. METHODS: This single-blind randomized controlled trial involved 60 currently pain-free individuals with a history of anterior knee pain and delayed (>10 ms) onset of VMO relative to VL during stair stepping. A blinded assessor took measures at baseline, immediately after 6 wk of treatment, and after an 8-wk follow-up. Both exercise programs involved weekly individual physiotherapy sessions with home exercises. The MCR program comprised specific VMO exercises incorporating EMG biofeedback, mostly in functional weight-bearing positions. The QS program comprised progressive-resistance inner range open kinetic chain exercises. The primary outcome was the latency between the onset of VMO EMG activity relative to that of VL during stair stepping measured using surface electrodes. RESULTS: During stair ascent, there was a significant change immediately after the intervention in VMO-VL timing in the MCR group only (P = 0.04), but there was no significant difference in the change between groups. During stair descent, VMO-VL timing changed in both groups (P < 0.01), with the MCR group showing a greater change than the QS group (P = 0.02). At the completion of training, quadriceps strength was only improved in the QS group (all P < 0.001). At follow-up, VMO timing and quadriceps strength had improved in both groups compared with baseline (P < 0.01), but there was no difference between groups. CONCLUSIONS: Although greater changes in motor control during stair descent and strength are induced by interventions that target each of these parameters in the short term, both parameters are similarly improved after the cessation of training, regardless of the target of the intervention.