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Abstract Given the importance of determining intervention-induced neuroplastic changes with lower extremity functional tasks, a reliable transcranial magnetic stimulation (TMS) methodology for proximal lower extremity muscles is needed. A pre-set fixed voltage value is typically used as the criterion for identifying a motor evoked potential (MEP) during the motor thresholding procedure. However, the fixed voltage value becomes problematic when the procedure is applied to proximal lower extremity muscles where active contractions are required. We sought to establish the reliability of a method measuring corticomotor excitability of gluteus maximus and vastus lateralis using normalized electromyography (EMG) as the criterion for identifying MEPs during the motor thresholding procedure. The active motor threshold for each muscle was determined using the lowest stimulator intensity required to elicit 5 MEPs that exceeded 20% maximal voluntary isometric contraction from 10 stimulations. TMS data were obtained from 10 participants on 2 separate days and compared using random-effect intra-class correlation coefficients (ICCs). Slopes from two input–output curve fitting methods as well as the maximum MEP of gluteus maximus and vastus lateralis were found to exhibit good to excellent reliability (ICCs ranging from 0.75 to 0.99). The described TMS method using EMG-normalized criteria for motor thresholding produced reliable results utilizing a relatively low number of TMS pulses.