A control system for an internal combustion engine is configured to suitably control the operation of electromagnetically driven intake valves and/or exhaust valves upon start-up of the engine for reducing the output current of a battery and suppressing a reduction in output voltage at minimum, thereby accurately operating the electromagnetically driven valves. The control system is operated such that when an ignition switch is turned on, the operation of a starter is prohibited and initial attraction for intake valves and exhaust valves is sequentially performed in such a manner that the attracting operations for the valves are not overlapped to each other; and after the initial attraction for all the valves is completed, the operation of the starter is permitted and the start-up of the engine is performed.