It is well documented that marked weakness of the quadriceps is present after knee joint injury. This joint trauma induces a presynaptic reflex inhibition of musculature surrounding the joint, termed arthrogenic muscle inhibition (AMI). The extent to which anterior cruciate ligament (ACL) injury affects thigh musculature motor unit activity, which may affect restoration of thigh muscle strength after injury, is undetermined. A randomized protocol of knee flexion and extension isometric contractions (10%-50% maximal voluntary isometric contraction) were performed for each leg on 54 subjects with electromyography array electrodes placed on the vastus medialis, vastus lateralis, semitendinosus, and biceps femoris. Longitudinal assessments for motor unit recruitment and average firing rate were acquired at 6-month intervals for 1 year post ACL injury. The ACL-injured population demonstrated smaller quadriceps and hamstrings motor unit size (assessed via motor unit action potential peak-to-peak amplitude) and altered firing rate activity in both injured and uninjured limbs compared to healthy controls. Motor unit activity remained altered compared to healthy controls at 12 months post ACL reconstruction (ACLR). Motor unit activity was altered after ACLR up to 12 months post-surgery. Further research is warranted to optimize rehabilitation interventions that adequately address altered motor unit activity and improve safety and success with return to sport after ACLR. In the interim, evidence based clinical reasoning with a focus on development of muscular strength and power capacity should be the impetus behind rehabilitation programming to address motor control deficits.