A control system for an internal combustion engine includes an exhaust gas purifying device, an exhaust gas temperature sensor, and temperature estimating device. The exhaust gas purifying device is provided to an exhaust duct of the internal combustion engine. The exhaust gas temperature sensor is provided in the exhaust duct on an upstream side of the exhaust gas purifying device. The temperature estimating device estimates a first exhaust gas temperature on a downstream side of the exhaust gas purifying device through a transfer function, which is expressed by a plurality of identical first-order lag elements, based on a second exhaust gas temperature on the upstream side of the exhaust gas purifying device sensed by the exhaust gas temperature sensor.