In a control system for a compression-ignition engine whose operation is switchable between a compression-ignition operation in which an air-fuel mixture supplied to a combustion chamber auto-ignites to burn owing to compression and a spark-ignition operation in which the air-fuel mixture is ignited to burn by a spark of a spark plug, it is determined whether a predetermined prohibitive condition to prohibit switching from the spark-ignition to the compression-ignition operation is satisfied, and switching from the spark-ignition operation to the compression-ignition operation is prohibited when the predetermined prohibitive condition is satisfied, thereby enabling to avoid premature ignition and misfire and to prevent drivability and fuel consumption performance from being affected therefrom.