This study was conducted to determine the effect of muscle energy technique (MET) on pelvic alignment, leg length, pain, and fatigue in chronic low back pain (CLBP) patients with leg length discrepancy (LLD). Forty-two CLBP patients with LLD volunteered to participate and were randomly assigned to the MET group ( = 21) and placebo group ( = 21). The intervention group performed three METs with 5 s of isometric contraction and 30 s of rest once, and the placebo group performed three times the placebo-MET, maintaining the same posture as the MET group without muscle isometric contraction. X-ray equipment, tape measure, and visual analog scale were used to evaluate pelvic alignment, leg length, pain, and fatigue before and after each intervention. In comparison pre- and postintervention, only the MET group showed significant changes in pelvic alignment, leg length, pain, and fatigue ( < 0.05). In comparison between groups, there were significant differences in all variables (pelvic alignment, leg length, pain, fatigue) ( < 0.05). The results of this study confirmed the therapeutic effect of MET for improving pelvic alignment, functional LLD, pain, and fatigue in CLBP patients with functional LLD. Future research is needed to evaluate the long-term effect on more chronic low back pain patients.