Leg-length discrepancy can cause not just issues in daily life, but functional problems such as abnormal walking, decreased balance, and musculoskeletal concerns. Squat exercises are highly stable and can exert a large for strength because the same strength is applied to both lower extremities. However, for a subject with leg-length discrepancy, balanced strength is not applied to the lower extremities; this can cause structural malalignment and unbalanced muscle activation. It is necessary to determine the influence of functional leg-length discrepancy on thigh muscle activation during squat exercises. Subjects with no leg-length discrepancy performed squats under two conditions—no leg-length discrepancy and simulated leg-length discrepancy with the left foot on a 3-cm-thick plate. We measured muscle activation of the vastus lateralis, vastus medialis, and medial and lateral hamstring by electromyography. The activations of the vastus lateralis and vastus medialis were significantly greater without leg-length discrepancy than with it (p<.05). Medial and lateral hamstring activation exhibited no significant difference. No muscles showed significant difference between the right and left legs in terms of activation under any condition. Therefore, leg-length discrepancy led to inefficiency in squat exercises and this factor should be removed prior to exercise.