Dysphagia is considered to be a significant barrier for recovery after lateral medullary infarction (LMI). However, there is still no gold standard treatment for dysphagia. The aim of this study was to explore an effect of an early treatment options for swallowing dysfunction after acute LMI. Medical records of acute LMI patients who had been admitted to the department of rehabilitation medicine from January 2014 to December 2017 were reviewed retrospectively. We compared the clinical efficacy of conventional dysphagia rehabilitation to early endoscopic intervention using either botulinum toxin injection into cricopharyngeal muscle or endoscopic balloon dilatation of the muscle. Outcomes, such as duration of parental feeding, albumin level at diet transition to enteral feeding, and complications, were analyzed. A total of 18 patients with LMI were included. While eight patients (8/9, 88.89%) in the endoscopic group were capable of orally ingesting their diet after intervention, the conversion from tube feeding to an oral diet was possible in only five patients (5/9, 55.56%) of the conventional group during hospitalization. However, the difference between the two groups was not significant (p-value ≤ 0.147, chi-square test). Only the final dietary level at the time of discharge was higher level in endoscopic group. The conversion interval from tube feeding to oral diet was also comparable between groups. There was no re-conversion from the oral diet to tube feeding in patients of either group during the median follow-up period of 20 months. Early endoscopic intervention may be a better option for dysphagia with LMI, compared to conventional dysphagia rehabilitation. However, a larger and prospective trial may be needed to confirm our observations.