Simultaneous occurrence of immune-based gastrointestinal diseases and autoimmune hepatitis, although not common, is of clinical importance. Some clinical and laboratory findings such as severe pruritus and elevated alkaline phosphatase raise suspicion of a biliary disease which overlaps autoimmune hepatitis. A strong clinical suspicion of overlap syndrome in a patient with autoimmune hepatitis prompts more diagnostic evaluations like MRCP, liver biopsy, and secondary laboratory tests. Patients who fall into the category of overlap syndrome proceed with timely monitoring of known complications including colorectal carcinomas, cholangiocarcinomas, and gallbladder cancers. It is strongly recommended that all simultaneous immune-based involvements be searched prior to labeling a patient as having pure autoimmune hepatitis. The current study attempted to express all challenges about a case with overlap syndrome referred to the gastroenterology ward of Taleghani Hospital and to review the latest articles and related guidelines about the diagnosis, treatment, complications, and surveillance of the mentioned patient with autoimmune hepatitis (AIH), primary sclerosing cholangitis (PSC), and inflammatory bowel disease (IBD).