<jats:p>Persistent quadriceps weakness after anterior cruciate ligament (ACL) reconstruction is a common hurdle to efficient rehabilitation. Therefore, we evaluated a new treatment strategy for athletes with ACL reconstruction. Eleven athletes with unilateral ACL reconstruction performed one set of flywheel Bulgarian split squats to exhaustion with a maximum knee extension of 60°, over 16 sessions, on their reconstructed limb. Quadriceps rate of force development (RFD) 0–50 ms (RFD0–50 ms), and 0–150 ms (RFD0–150 ms), maximum voluntary isometric contraction (MVIC), and central activation ratio (CAR) were measured bilaterally on the week before and after the intervention. In the reconstructed limb, the RFD0–50 ms (p = 0.04; Cohen’s d = 0.8) and RFD0–150 ms (p = 0.03; d = 0.9) increased after training. Before-after changes in MVIC and CAR were not significant (p > 0.05), but the lower the baseline MVIC, the greater the gain in MVIC (r = −0.71, p = 0.02). The between-leg difference in MVIC changed from large before (p = 0.01; d = 0.8) to small after training (p = 0.04; d = 0.4). One set of deep knee flexion flywheel Bulgarian split squats to exhaustion improved quadriceps deficits in well-trained athletes with ACL-reconstruction, particularly those with relatively low quadriceps force production.</jats:p>