Disclosed herein is a method of preparing an alloy catalyst for fuel cells, which is suitable for mass production and can reduce manufacturing costs. The method includes vaporizing at least two catalyst precursors in separate vaporizers; supplying the at least two vaporized catalyst precursors to a reactor while preventing contact therebetween; and synthesizing an alloy catalyst in the reactor. The method can prepare an alloy catalyst through a one-step process unlike typical multi-step methods for preparing catalysts, and can prepare an alloy catalyst at a much lower temperature than the typical methods for preparing alloys, thereby enabling mass production and cost reduction.