Aspiration pneumonia is the most common cause of death in patients with percutaneous endoscopic gastrostomy (PEG) and nasogastric tube (NGT) feeding. This study aimed to compare PEG versus NGT feeding regarding the risk of pneumonia, according to the severity of pooling secretions in the pharyngolaryngeal region. Patients were stratified by endoscopic observation of the pooling secretions in the pharyngolaryngeal region: control group (<25% pooling secretions filling the pyriform sinus), pharyngeal group (25-100% pooling secretions filling the pyriform sinus), and laryngeal group (pooling secretions entering the laryngeal vestibule). Demographic data, swallowing level scale score, and pneumonia requiring hospital admission were recorded. Patients with NGT ( = 97) had a significantly higher incidence of pneumonia (episodes/person-years) than those patients with PEG ( = 130) in the pharyngeal group (3.6 ± 1.0 vs. 2.3 ± 2.1, < 0.001) and the laryngeal group (3.8 ± 0.5 vs. 2.3 ± 2.2 vs, < 0.001). The risk of pneumonia was significantly higher in patients with NGT than in patients with PEG (adjusted hazard ratio = 2.85, 95% CI: 1.46-4.98, < 0.001). Cumulative proportion of pneumonia was significantly higher in patients with NGT than with PEG for patients when combining the two groups (pharyngeal + laryngeal groups) ( = 0.035). PEG is a better choice than NGT feeding due to the decrease in risk of pneumonia requiring hospital admission, particularly in patients with abnormal amounts of pooling secretions accumulation in the pyriform sinus or leak into the laryngeal vestibule.