A self-cleaning burner system incorporates an automatic clean cycle when the burner is started up. Cycles may be programmed for once-a-day cleaning cycle or for other desired interval. On start-up, the cycle routes a small amount of fuel to the burner for ignition inside the burner to clean the burner surfaces. The system incorporates an igniter for fast, routine, and safe ignition of the fuel. Thus, small amounts of debris that accumulate on a surface burner are automatically ignited when the burner is started, keeping the burner clean and operating at a high state of efficiency at all times. The self-cleaning burner system may be incorporated into a fryer or other heating appliance for reliable, efficient operation.