An auto ignition type autothermal reformer (ATR) performs reproducible ignition using a catalyst that performs ignition without a separate ignition unit, such as an igniter or heating wire, and a fuel cell system having the ATR. The ATR includes a reaction container having a first opening through which a fuel is introduced into the reaction container and a second opening through which a reformate is discharged from the reaction container, the fuel having a mixture of an aqueous primary fuel solution and hydrogen peroxide; a first catalyst disposed adjacent to the first opening in the reaction container, the first catalyst being a granular catalyst; a second catalyst disposed at the rear portion of the first catalyst to promote an autothermal reforming reaction; and a third catalyst disposed at the rear portion of the second catalyst to promote an oxidation reaction.