An intake air control system for an engine having an air intake passage, a throttle valve in the intake passage and an intake valve for selectively opening and closing communication between the intake passage and a cylinder. The control system determines target intake passage pressure and target intake air amount in accordance with engine operating conditions. A target throttle opening is set in accordance with both the target pressure and the target intake air amount. The throttle valve is then driven to the target opening. Intake passage pressure is detected and a target intake valve open/close timing is determined in accordance with both the detected intake passage pressure and the target intake air amount. The intake valve is then driven in accordance with the target open/close timing.