The aim of this study was to establish whether there are any electromyographic (EMG) differences after two different surgical techniques in two years follow-up after anterior cruciate ligament (ACL) reconstruction. Study participants were divided into three groups. The control group included healthy athletes (C), the first study group (E1) consisted of injured athletes who were treated by ACL reconstruction using patellar tendon graft and the second study group (E2) comprised injured athletes treated by gracilis and semitendinosus tendon graft. The threshold of muscle activity was defined as 30% of maximum amplitude of EMG signal medial envelope of individual muscles in the control group. Two years after reconstruction, the E2 group achieved the maximum amplitude of biceps femoris muscle signal in the takeoff phase statistically significantly later than the E1 group (0.0166, p = 0.05 and 0.015152, p = 0.05/3 = 0.016), whereas the rectus femoris muscle in the flight phase in the E2 group improved statistically significantly earlier than in the C group (0.0393, p = 0.05 and 0.025974, p = 0.05/3 = 0.016). The results of this study show particularly statistically significant differences between observed surgery techniques, which led to the change of the neuromuscular pathway during simple and controlled knee movements even two years after ACL reconstructions in athletes who returned to active training. These disturbances of muscle work coordinations in the knee joint could be tied to the function and location from which the graft was taken rather than the quality of the transplant itself. This may result in an increased risk of repeated knee injury, including potential permanent health consequences in athletes. Based on the results of this research, we were unable to establish which of the presented ACL reconstruction techniques is more appropriate. This study may be useful for athletes and their coaches, who could plan, programme and adequately adjust their training process, thereby improving knee function in the best possible way, which in turn would maintain and extend athletes' respective sports careers.