Objective Although transcranial magnetic stimulation (TMS) has been widely used to study motor cortex organization and excitability, the reliability of this technique has not been thoroughly investigated. Furthermore, previous reports of TMS reliability have been restricted to upper limb musculature. We sought to determine the test–retest reliability for TMS mapping of motor representations for swallowing musculature. Methods Twenty healthy volunteers were tested twice over two weeks using TMS to determine motor threshold, map area, map volume, maximal MEP site location and maximal MEP site size for the suprahyoid complex and pharyngeal musculature. Results Good test–retest reliability was found in both swallowing muscle sites for the following test parameters: motor map area, maximal MEP site location: lateral coordinate, maximal MEP site size and motor threshold (ICC = 0.76–0.98). Moderate reliability was observed for motor map volume and maximal MEP site location: anterior–posterior coordinate (ICC = 0.68–0.74). Conclusions TMS assessments of motor representation size, location and excitability appear to be highly reproducible, although the reliability of these measures may vary according to the specific muscle under investigation. Significance These works provide much needed psychometric data to validate the use of TMS to assess the cortical representation of swallowing musculature.