An control apparatus and method for an engine having a turbocharger may include determining a load condition of the engine by a controller, and opening and closing an intake valve, a throttle valve, and a wastegate valve by the controller according to the load condition of the engine, where a combustion chamber generates power by combusting a fuel, an intake valve adjusts an air/fuel mixed gas flowed into the combustion chamber, a continuously variable valve timing apparatus advances or retards an opening/closing timing of the intake valve, a turbocharger having a turbine and a compressor compressing air flowed into the combustion chamber, a throttle valve adjusting air supplied to the combustion chamber, a wastegate valve adjusting the exhaust gas flowed into the turbine, and a controller controlling the intake valve, the throttle valve, and the wastegate valve according to a load region of the engine.