A valve control system for an internal combustion engine, which enables the operating mode of a valve system to be switched in optimal timing while preventing the driver from feeling the switching operation so busy and at the same time securing feeling of acceleration, thereby improving drivability. A variable valve-actuating mechanism is capable of selectively switching the operating mode of a valve system including intake valves and an exhaust valve between a plurality of operating modes different in output characteristics. Whether or not the operating mode of the valve system should be switched is determined. The execution of the switching of the operating mode of the valve system based on the determination is suppressed according to a degree of suppression set depending on detected load on the engine.