A 63-year-old woman was referred to Fukushima Red Cross Hospital with an enlargement of the left submandibular gland and subcutaneous bleeding in the chest and legs. A diffuse enlargement of the pancreas was also detected by abdominal computed tomography, and laboratory data showed severe thrombocytopenia. She was diagnosed with IgG4-related disease (IgG4-RD) complicated with autoimmune thrombocytopenia and was treated with methylprednisolone, after which the number of platelets favorably increased. Further investigation for liver dysfunction revealed underlying primary biliary cirrhosis (PBC). We herein report a rare case of IgG4-RD overlapping PBC complicated with autoimmune thrombocytopenia.