A method of sterilizing a water supply apparatus according to the present invention, in a method of sterilizing the water supply apparatus by a sterilizer, includes generating sterilizing water in a manner of electrolyzing purified water, sterilizing water tanks, passages and a water cock of the water supply apparatus by circulating the sterilizing water, draining out hot water, sterilizing a hot water tank, draining out the entire sterilizing water, rinsing the water tanks, the passages and the water cock, and draining out rinsing water.