Disclosed is a controller for a turbocharged engine. The engine includes a supercharger configured to supercharge intake air using an exhaust gas from the engine, and including movable flaps arranged so that a boost pressure generated in an intake passage is adjustable. If a rotational speed of a turbine and compressor that constitute the supercharger has reached a first threshold lower than an endurance limit, an amount of fuel injected to the engine is reduced to a predetermined amount. If the rotational speed has reached a second threshold lower than the first threshold, the amount of fuel injected is reduced in accordance with an excess of the rotational speed over the second threshold.