A cathode catalyst for a fuel cell includes an Ru—Se alloy having an average particle size of less than or equal to 6 nm. The Ru—Se alloy is amorphous catalyst. A membrane electrode assembly and a fuel cell system include the cathode catalyst. A catalyst for a fuel cell is prepared by drying a ruthenium solution including a water-soluble ruthenium precursor to obtain a first dried product; subjecting the first dried product to a first heat-treatment to obtain a heat-treated product; adding an Se solution including a water-soluble Se precursor to the heat-treated product to obtain a mixture; drying the mixture to obtain a second dried product including ruthenium and Se; and subjecting the second dried product to second heat-treatment.