Aspiration prevention surgeries, such as laryngotracheal separation and total laryngectomy are performed to prevent aspiration pneumonia. We aimed to investigate the outcomes of surgery for intractable aspiration and relevant factors. This retrospective cohort study used a nationwide insurance claims database that included company employees and their family members aged < 75 years in Japan. We extracted the data of patients who underwent aspiration prevention surgeries between January 2005 and March 2019. We identified 127 patients (males, 55.9%), of whom 59.8% were aged < 18 years at the surgery. The most common comorbidity was neurological disease (99.2%). The frequency of pneumonia episodes decreased by 1.5 per year after surgery compared with before surgery (p < 0.001). Among patients who received parenteral and enteral nutrition before surgery (n = 92), the adjusted hazard ratio (aHR) for oral intake without parenteral and enteral nutrition was lower in the longer preoperative duration (≥ 14.7 months) for the parenteral and enteral nutrition. However, the difference was not statistically significant (aHR 0.55; 95% confidence interval: 0.15-2.08, p = 0.38). The aHR for oral intake was higher in the ≥ 30 years group than in the < 30 years group (aHR 13.76; 95% confidence intervals: 4.18-42.24; p < 0.001). This study demonstrated that postoperative oral intake was achieved more frequently in patients aged ≤ 30 years than in those aged > 30 years, and supported the effectiveness of aspiration prevention surgery for reducing aspiration pneumonia. Further research is necessary to investigate factors related to postoperative oral intake.