Introduction Autoimmune hepatitis (AIH) is a common pediatric liver disease and long-term remission is usually maintained with low dose prednisolone and azathioprine (AZA). The aim of this study is to evaluate the efficiency of AZA monotherapy for maintenance treatment of children with AIH. Materials and methods This study was a retrospective analysis of the 55 children with AIH. Patients were divided into two groups: combination therapy (CT) and AZA group based on maintenance therapy. Results of these two different maintenance treatments were compared in children with AIH. Results The mean age of the children was 10.67 +/- 4.30 years (61.8% females) with a mean follow-up period of 46.8 +/- 33.6 months. For maintenance treatment, 39 (70.9%) patients received AZA and 16 (29.1%) patients received CT. Relapse was observed in nine (19.6%) cases in the follow-up period; two were in the CT group (2/16; 12.5%) and seven (7/39; 17.9%) were in the AZA group (P = 0.620). In AZA group, the duration of remission was 22.2 +/- 6.1 months and that was longer than CT group (P = 0.025). Conclusion Our study suggests that AZA monotherapy is an effective and safe therapy for maintaining remission in children with AIH. AZA monotherapy may be used for maintenance treatment of children with AIH, except in cases of overlap syndrome and also to avoid side effects of long-term used steroids and to improve treatment compliance in proper cases.