Muscle strain injuries (MSIs) in the hamstrings are among the most prevalent injuries in elite soccer. We aimed to examine the relation between biomechanical maladaptation in eccentric strength and neuromuscular factors separated by their time and frequency domains. 20 elite soccer players with a previous history of unilateral MSI in the M. biceps femoris (BF) long head and 20 without MSI participated. Knee flexion torques, rate of torque development (RTD) and electromyographic signals (EMG) of the BF, the M. semitendinosus (SMT) and knee extensors were obtained during unilateral maximal eccentric knee flexions performed at slow (30°/s) and fast (120°/s) angular speeds. Root mean squares and mean power frequency (MF) was calculated. In the group with a history of MSI, reduced maximal eccentric flexion torque (slow eccentrics -8±11, p<0.05; fast eccentrics -18±13 N*m, p<0.05) and RTD (-33±28 N*m/s, p<0.05; -95±47 N*m/s, p<0.05) concomitantly occurred with diminished agonistic myoelectrical activities (-4±5% of MVC, p<0.05; -10±7% of MVC, p<0.05) and MFs (-24±13 Hz, p<0.05; -24±18 Hz, p<0.05) in the BF. Simultaneously, antagonistic myoelectric activity was elevated (+4±3% of MVC, p<0.05; +3±3% of MVC, p<0.05) in MSI affected legs as compared to unaffected legs for both eccentric contractions. Deficits in myoelectrical activity (r2 = 0.715, p<0.05; r2 = 0.601, p<0.05) and MF (r2 = 0.484, p<0.05; r2 = 0.622, p<0.05) correlated with deficits in maximal torque in the affected leg in the MSI group. Analysis of SMT demonstrated no significant differences. Positive relationships between neuromuscular deficits and the reduced eccentric strength profile underpin neuronal inhibition after MSI. This persistent involvement of dysfunctional synergist and antagonist neural hamstring function in strength weakness is of clinical relevance in sports medicine for prevention and rehabilitation.