An intake control system for an internal combustion engine, which is capable of suppressing a change in an intake pressure caused by a change in a target intake air amount even in a transient operating condition in which the target intake air amount is varied, thereby making it possible to control the intake pressure stably and accurately. The intake control system controls an intake air amount by an intake valve lift, and controls intake negative pressure by a throttle valve. The system limits a target intake air amount based on upper and lower limit values set according to the intake valve lift and an intake cam phase, and corrects the target intake air amount by averaging the same using averaging calculation such that the change therein is delayed. A throttle valve opening is set according to the corrected target intake air amount.