Prominent dysphagia is seen among patients with spinal muscular atrophy (SMA) type 2, especially at the late stage of their disease progression. Nasogastric tube feeding and gastrostomy are commonly utilized to maintain their nutritional status. However, choosing a treatment strategy to maintain appropriate nutritional status is often complicated by multiple factors, such as physical conditions and social aspects. We report a 21-year-old man with SMA type 2 who has been suffering from severe dysphagia. The findings at video-fluoroscopic swallow study (VSS) were consistent with a diagnosis of cricopharyngeal dysphagia. His dysphagia was successfully treated with percutaneous injection of botulinum toxin A (BTA) into the cricopharyngeal muscle. Our result demonstrates that administration of BTA is one of the effective treatment choices for dysphagia in SMA patients.