Motor evoked potentials (MEPs) recorded from pharyngeal and anterior hyo-mandibular (submental) muscles at rest have been used to evaluate treatment effects on neural pathways underlying swallowing. This study documents a novel methodological approach of recording reliable intra- and inter-session MEPs at the submental muscle group during task-related volitional swallowing. MEPs were elicited by single-pulse transcranial magnetic stimulation (TMS), triggered by a custom-made system when a pre-set level of surface electromyographic activity in the target muscles was breached. Fifteen MEPs were recorded during each of four sessions. Intraclass correlation coefficients (ICCs) were used to assess test-retest reliability within and across sessions for blocks of 3, 5, 10 and 15 trials. Highly reliable intra-session reliability was achieved, maximal for blocks of five trials (0.915). Inter-session reliability varied between 0.474 (three trials per block) and 0.909 (10 trials per block). Surface electromyography-triggered TMS allows reliable measurement of MEP amplitude at the submental muscle group within and across sessions when muscles are pre-activated during volitional swallowing. This methodology will be useful for future investigations on the effects of pathology and modulation of swallowing neural pathways.