An apparatus for controlling an engine includes: an engine with a cylinder; a throttle valve to adjust a flow rate of intake air supplied to the cylinder; a supercharger to supply supercharged air to the cylinder; an intake valve to supply intake air by selectively opening and closing the cylinder; a variable valve timing device to adjust opening and closing timings of the intake valve; a variable valve duration device to adjust an opening duration of the intake valve; and a controller to adjust the amount of air inside of the cylinder by fixing an intake valve opening (IVO) timing and adjusting an intake valve closing (IVC) timing through the variable valve timing device and the variable valve duration device from a time at which a demanded torque is input to a time at which the demanded torque is followed by the throttle valve or the supercharger.