An engine control system having primary and secondary fuel tanks comprises a fuel monitoring module and a transfer pump (TP) diagnostic module. The fuel monitoring module determines a measured fuel level of the secondary fuel tank based on a fuel level signal received from a fuel level sensor when a fuel TP is on for greater than a predetermined time period required for the fuel TP to reduce the measured fuel level from a predetermined fuel level to below the predetermined fuel level. The TP diagnostic module diagnoses a condition of the fuel TP based on the measured fuel level.