The professional activity of high performance, or elite sportsmen involves loads approaching extreme exertion, which often leads to injuries of the lower limbs. Anterior cruciate ligament (ACL) injury is one of the most common types of knee injuries. This study aimed to evaluate the effectiveness of a comprehensive rehabilitation program for athletes that underwent arthroscopic ACL reconstruction. The study involved 64 athletes aged from 17 to 31 years. Treatment group participants were offered a comprehensive medical rehabilitation program that included isokinetic training sessions on the TECNOBODY IsoMove biomechanical exercising machine; the sessions followed a purpose-designed method. The results of medical rehabilitation of the athletes were assessed through gait analysis done with a DIERS Motion 4D complex. The assessments took place 8 and 15 weeks after the reconstruction. At 8 weeks after the surgery, gait analysis parameters revealed no significant differences between the groups. Fifteen weeks after the reconstruction, when treatment group (TG) members were through all the isokinetic training sessions, the results were as follows: for the Stand Time parameter, the operated limb (OL) support deficit was 0.04% compared to the healthy limb (HL) support, and for the Single Limb Support parameter it was 3.71%, while in the control group (CG) that had no isokinetic training sessions the values were 12.44% and 18.55%, respectively.  As for the Swing Time parameter, TG participants showed the deficit of HL transfer symmetry (relative to OL) of 3.99%, while the value of this parameter in the CG was 20.54%. The difference is significant, which proves the effectiveness of the developed isokinetic training method as part of the comprehensive medical rehabilitation program, the application of which resulted in faster recovery of muscle strength and compromised walking-associated support and locomotor functions in TG athletes.