The present study aimed to examine and compare the effects of a rehabilitation exercise (RE) using neuromuscular electrical stimulation (NMES) and blood flow restriction (BFR) on muscle function and knee functional abilities in patients who underwent anterior cruciate ligament reconstruction (ACLR). A total of 45 patients who underwent ACLR (28.76 ± 0.8 years; 34 males and 11 females) were retrospectively divided into three groups: control (CON, n = 15), NMES (n = 15), and BFR (n = 15). All participants carried out the RE program for 60 min, thrice a week for 12 weeks. The Lysholm score, International Knee Documentation Committee (IKDC) subjective score, thigh circumference at 5 cm from the knee joint, Y-balance posterior medial, and lateral significantly increased in all groups via intervention (p < 0.05). However, NMES showed a higher thigh circumference at 15 cm from the knee joint than CON via intervention (p < 0.05), and the strength and endurance of quadriceps femoris and hamstrings and Y-balance anterior showed a significant increase via intervention in NMES and BFR compared with CON (p < 0.05). In conclusion, we confirmed that RE using NMES and BFR effectively enhances muscle function and balance in ACLR patients.