A 37-year-old woman who had previously been diagnosed with idiopathic chronic intestinal pseudo-obstruction (CIPO) at another hospital was admitted to our institution with severe abdominal pain. She had a history of several abdominal surgeries to treat ileus at the previous hospital, and contrast-enhanced computed tomography on admission revealed subileus without any apparent causes of obstruction. Total parenteral nutrition, a gastrointestinal prokinetic agent, and opiates reduced persistent pain;however, breakthrough pain continued. A neurologist at our hospital suggested autoimmune autonomic ganglionopathy (AAG) as a potential cause of CIPO. The patient was diagnosed with suspected AAG on the basis of seropositive results for anti-ganglionic acetylcholine receptor antibody. Intravenous immunoglobulin administration and plasma exchange were performed in combination with immunosuppressive drugs;however, her symptoms barely improved. Although percutaneous endoscopic gastrostomy and enterostomy were subsequently performed to reduce internal intestinal pressure, her pain relief was insufficient.