We present a rare case of a 50-year-old woman with simultaneous primary biliary cholangitis (PBC) and autoimmune hyperthyroidism in which the factors associated with liver dysfunction were evaluated over a 3year follow-up period. Although serum thyroid hormone levels improved after the administration of thiamazole, thyroid dysfunction was not directly associated with liver dysfunction. During the follow-up period, anti-hyperlipidemic drug therapy and eradication therapy for Helicobacter pylori (HP) infection caused transient elevation of serum transaminase levels. It should be recognized that serum liver enzyme levels might be affected by various factors, including the therapies for the many complications of PBC.