Purpose: Reliability of motor-evoked potential threshold and amplitude measurement of upper limb muscles is important when detecting changes in cortical excitability. The objective of this study was to investigate intra-rater, test-retest reliability and minimal detectable change of resting motor threshold and amplitude of a proximal and distal upper limb muscles, anterior deltoid and distal extensor digitorum communis in healthy adults. Method: To measure motor-evoked potential responses, transcranial magnetic stimulation was interfaced with electromyography and neuronavigation equipment. Two measurements were conducted on day 1 and a third measurement three days later. Reliability was analysed using intraclass correlation coefficients. Results: Twenty participants completed the study. Excellent intra-rater (intraclass correlation coefficient = 0.91 (extensor digitorum), 0.94 (anterior deltoid)) and good to excellent test-retest reliability (intraclass correlation coefficient = 0.69 (anterior deltoid), 0.84 (extensor digitorum)) was found for resting motor threshold. Minimal detectable change for resting motor threshold was found at 10.95% (extensor digitorum) and 16.35% (anterior deltoid) between first and third measurements. Motor-evoked potential amplitude of extensor digitorum communis had fair to good intra-rater (intraclass correlation coefficient = 0.50) and test-retest reliability (intraclass correlation coefficient = 0.65). Conclusions: Our results suggest that resting motor threshold is a reliable neurophysiological measure even for proximal shoulder muscles. Future research should further explore the reliability of motor-evoked potential amplitude before integration into neurological rehabilitation.