A 55-year-old woman was admitted to our hospital with acute hepatitis of unknown origin. She had a history of incomplete-type CREST (calcinosis, Raynaud phenomenon, esophageal dysmotility, sclerodactyly, and telangiectasia) syndrome and chronic thyroiditis approximately 10 years earlier. Although she achieved spontaneous remission without treatment, she was re-admitted 18 months later due to recurrent liver dysfunction. Liver biopsy was performed as we strongly suspected autoimmune hepatitis despite her normal serum immunoglobulin G level. Liver biopsy findings were histologically compatible with autoimmune hepatitis, and administering prednisolone (30 mg/day) led to a prompt recovery of her liver dysfunction. No relapse occurred during the tapering of prednisolone to a maintenance dose of 5 mg/day. Here we report a rare case of autoimmune hepatitis in a patient with a history of incomplete-type CREST syndrome and chronic thyroiditis.