A variable valve control system for an internal combustion engine, includes a valve to open and close an opening of a combustion chamber of the engine, a variable lift characteristic control mechanism to adjust a valve lift characteristic of the valve, a sensing section to collect information needed to determine an estimated valve lift characteristic of the valve, an input section to receive an externally input calibration-mode command. The variable valve control system is configured to perform: controlling the valve lift characteristic to be a mechanically defined small setting in response to the calibration-mode command; collecting the information when the valve lift characteristic is the small setting; and calibrating the sensing section in accordance with the collected information.