The objective of this study was to investigate the outcomes of rehabilitation (with swallowing therapy) after percutaneous endoscopic gastrostomy (PEG) in patients with neurogenic dysphagia. Forty-seven patients (29 males and 18 females) who were transferred to the rehabilitation ward of our hospital after receiving PEG tube placements during a 5-year period were enrolled in this study. Patients’ demographic data, comorbidities, nutritional statuses, and laboratory biomarkers before the PEG procedure were collected. Rehabilitation (with swallowing therapy) outcomes such as changes in Functional Independence Measure (FIM) and dysphagia grade (using Fujishima’s classification) were evaluated. Significant improvements in FIM scores and dysphagia grades after rehabilitation therapy were observed. Twenty-seven patients (57.4 %) were discharged with some oral intake and 10 patients (21.3%) were discharged PEG-free (defined as the PEG tube not being used or removed). Factors associated with being discharged with some oral intake were increase in FIM score (adjusted OR 1.10, 95 % CI 1.02–1.19) and higher baseline dysphagia grade (adjusted OR 1.88, 95 % CI 1.04–3.39). Factors associated with being discharged PEG-free were longer rehabilitation period (OR 1.03, 95 % CI 1.01–1.04), absence of respiratory disorders (OR 0.12, 95 % CI 0.03–0.35), and increase in FIM score (OR 1.17, 95 % CI 1.08–1.28). Changes in dysphagia grade were significantly correlated with changes in FIM score (r 2 = 0.46, p < 0.0001), indicating that improvement of FIM scores through general rehabilitation therapy may play an important role in the treatment of dysphagia.