The study aimed at investigating the effects of neuromuscular electrical stimulation superimposed on functional exercises (NMES+) early after anterior cruciate ligament reconstruction (ACLr) with hamstring graft, on muscle strength, knee function, and morphology of thigh muscles and harvested tendons. Thirty-four participants were randomly allocated to either NMES+ group, who received standard rehabilitation with additional NMES of knee flexor and extensor muscles, superimposed on functional movements, or to a control group, who received no additional training (NAT) to traditional rehabilitation. Participants were assessed 15 (T1), 30 (T2), 60 (T3), 90 (T4) and at a mean of 380 days (T5) after ACLr. Knee strength of flexors and extensors was measured at T3, T4 and T5. Lower limb loading asymmetry was measured during a sit-to-stand-to-sit movement at T1, T2, T3, T4 and T5, and a countermovement-jump at T4 and T5. An MRI was performed at T5 to assess morphology of thigh muscles and regeneration of the harvested tendons. NMES+ showed higher muscle strength for the hamstrings (T4, T5) and the quadriceps (T3, T4, T5), higher loading symmetry during stand-to-sit (T2, T3, T4, T5), sit-to-stand (T3, T4) and countermovement-jump (T5) than NAT. No differences were found between-groups for morphology of muscles and tendons, nor in regeneration of harvested tendons. NMES+ early after ACLr with hamstring graft improves muscle strength and knee function in the short- and long-term after surgery, regardless of tendon regeneration.