A control system for an internal combustion engine includes: a fuel amount detector; a smoothing calculation unit that calculates a smooth output value, which is obtained by smoothing an output value of the fuel amount detector in a temporal direction; a continuous low speed condition detection unit that detects a continuous low speed condition in which the vehicle speed remains in the low speed region continuously beyond a predetermined time period; a calculation processing unit that successively calculates a maximum value and a minimum value of the smooth output value; a reference setting unit that updates and stores a reference value in response to the engine stoppage and in accordance with the current minimum value calculated by the calculation processing unit; and a fuel supply determination unit that detects a fuel supply to the fuel tank during the continuous low speed condition.