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.