The purpose of this study is to determine whether neuromuscular electrical stimulation of the suprahyoid muscle is effective compared to that of the infrahyoid muscle in brain-injured patients with dysphagia. A total of 132 patients with stroke, traumatic brain injury, or brain tumor in 2 university hospitals were allocated to 2 groups: those who received electrical stimulation therapy (EST) on the suprahyoid muscles (SM group, n = 66) and those who received EST with one pair of electrodes on the suprahyoid muscle and the other pair on the infrahyoid muscle (SI group, n = 66). Patients received 11.2 ± 3.4 sessions of electrical stimulation in the SM group and 11.9 ± 3.4 sessions in the SI group. The functional dysphagia scale (FDS), swallow function score (SFS), supraglottic penetration, and subglottic aspiration were measured using videofluoroscopic swallowing study. FDS scores decreased from 42.0 ± 19.1 to 32.3 ± 17.8 in the SM group and from 44.8 ± 17.4 to 32.9 ± 18.8 in the SI group by per-protocol (PP) analysis, and those decreased from 41.2 ± 20.9 to 34.5 ± 20.3 in the SM group and from 44.3 ± 19.1 to 35.7 ± 20.5 in the SI group by intention-to-treat (ITT) analysis, after electrical stimulation (p < 0.001 for each). SFSs increased from 3.3 ± 1.8 to 4.2 ± 1.6 in the SM group and from 2.8 ± 1.8 to 4.0 ± 1.8 in the SI group by PP analysis, and those increased from 3.3 ± 1.6 to 3.9 ± 1.6 in the SM group and from 2.8 ± 1.9 to 3.6 ± 2.0 in the SI group by ITT analysis, after electrical stimulation (p < 0.001, respectively). However, changes in FDS scores, SFSs, penetration, and aspiration were comparable between the SM and the SI groups. The results suggest that both SM and SI therapies induced similar improvements in swallowing function in brain-injured patients.