We investigated the capacity for dysphagia prognosis prediction using diffusion tensor tractography (DTT) to assess the state of the corticobulbar tract (CBT) during the initial period following lateral medullary infarction (LMI). Twenty patients with LMI and 20 control subjects were recruited for this study. The patients were classified into two subgroups: subgroup A (16 patients with nasogastric tube required for six months or less after LMI onset) and subgroup B (4 patients with nasogastric tube required for more than six months after onset). DTT was used to reconstruct the CBTs of each patient and control subject, and the fractional anisotropy (FA) and tract volume (TV) measurements were obtained. In the affected hemisphere, the FA value of the CBT was significantly lower in subgroup B than in subgroup A and the control group (p < 0.05), with no significant difference between subgroup A and the control group. In the affected and unaffected hemispheres, the TV values of CBT in subgroups A and B were lower than those of the control group (p < 0.05), with no significant difference between subgroups A and B. In addition, among the four patients of subgroup B, reconstruction of the CBT was not possible in three patients, and the remaining patients exhibited on old lesion in the corona radiate involving descending pathway of the CBT in the affected hemisphere. We found that the injury severity of the CBT in the affected hemisphere appeared to be related to a poor dysphagia prognosis following LMI. Our results suggest that evaluation of the CBT state during the early post-LMI could be useful for dysphagia prognosis prediction.