Objectives: Rupture of the anterior cruciate ligament (ACL) is a severe injury common in sports. It also has a high rate of re-injury. The aim of this work was to assess hamstring muscle fatigue in active football players after ACL reconstruction who were cleared to play and to determine symmetry between the lateral and medial hamstring muscles. Methods: In professional football players post ACL reconstruction (n = 25) and non-injured players (n = 26), the bioelectrical activity of the medial (biceps femoris—BF) and lateral (semimembranosus and semitendinosus—SEM) hamstring muscles was measured during 60 s of isometric contraction. The fatigue variables were calculated using the Continuous Wavelet Transform (CWT) tool. Results: The football players following ACL reconstruction demonstrated significant asymmetry in fatigue of the lateral and medial hamstring muscles, with greater fatigue in the SEM compared to the BF muscle. Moreover, in those after reconstruction, the changes are more pronounced, with higher muscle fatigue in both limbs (they have lower MDF than non-injured players) and more severe SEM muscle insufficiency (noted in both limbs but with greater intensity in the non-operated one). Conclusions: The higher SEM muscle fatigue observed in this study influenced the lateral-to-medial activation ratio within the hamstring muscle, which may be a probable cause of this muscle’s insufficiency in laterally stabilizing the knee in the frontal and transverse plane. Furthermore, the hamstring muscles after reconstruction were more fatigued in both limbs, which may be another risk factor for ACL graft rupture. Therefore, increased fatigue in specific hamstring muscles may indicate the direction in which knee stabilization is compromised due to ACL overload. A muscle that becomes fatigued and inefficient more quickly also becomes ineffective in performing its function sooner, which can lead to increased overloading forces acting on the ACL graft.