We experienced a living donor liver transplantation for a 26-month-old girl with complement factor H deficiency. Complement factor H is a plasma protein that regulates the activity of the complement pathway. Complement overactivity induced by complement factor H deficiency is associated with atypical hemolytic uremic syndrome. Liver transplantation can be the proper treatment for this condition. During the liver transplantation of these patients, prevention of the complement overactivation is necessary. Minimizing complement activation, through the use of modalities such as plasma exchange before the surgery and transfusion of fresh frozen plasma throughout the entire perioperative period, may be the key for successful liver transplantation in these patients.