A 75-year-old man with multiple system atrophy received percutaneous endoscopic gastrostomy (PEG) because of dysphagia. But recurrent aspiration pneumonia occurred after PEG nutrition, which was due to gastroesophageal reflux. As he had floppy epiglottis, orally inserted endoscopic procedure caused upper airway obstruction, which required transient non-invasive positive-pressure ventilator (NIPPV) treatment. He underwent transgastrostomal jejunal tube (PEG-J) replacement under the nasal endoscopic guidance successfully, but tube was patent only for 5-months. Thereafter, endoscopic jejunostomy (PEJ) via gastric stoma was performed on NIPPV safely, and the patient is now stable. For the management of nutrition in the advanced stage of neurodegenerative disease patients, PEJ is one of useful choice.