The present invention is related to an apparatus for and a method of controlling an engine provided with: a variable operation angle mechanism that is provided for varying a valve operation angle of an engine valve driven by a camshaft, and is capable of varying a center phase of the valve operation angle in response to a variation in the valve operation angle; and a variable valve timing mechanism provided for varying a rotating phase of the camshaft relative to a crankshaft of the engine, in which a target valve operation angle and a target rotating phase is calculated based on the engine operating state, and a correction value for correcting the target rotating phase based on the target valve operation angle is set. Then, the target rotating phase is corrected by the correction value, thereby controlling the variable valve timing mechanism based on the corrected target rotating phase.