For accurately estimating an air quantity flowing into a cylinder at the time of operating an intake control valve, a control apparatus for an engine according to the present invention is provided with an intake control valve which can open/close an intake passage in synchronization with opening/closing of an intake valve, intake control valve controlling means which opens the intake control valve in the midst of the intake stroke and thereafter, closes the intake control valve, and air quantity estimating means which estimates an air quantity flowing into a cylinder after the intake control valve has opened, based upon opening timing of the intake control valve, closing timing or an opening period of the intake control valve, and a pressure at a downstream side of the intake control valve at the opening timing of the intake control valve.