An engine control system comprising a variable valve actuating mechanism for an engine which may consists of a mechanism capable of varying valve timing, a variable capacity supercharger which may consists of a turbocharger provided with moveable vanes for varying a cross sectional area of an exhaust gas passage leading to a turbine wheel, and a control unit for controlling a valve actuating operation of the valve actuating mechanism and a capacity varying operation of the variable capacity supercharger. The capacity of the supercharger is controlled by taking into account the operating conditions of the valve actuating mechanism. Thus, the control unit is capable of achieving a precise and prompt control action, and, by appropriately determining the control plan, it is possible to increase the maximum output of the engine and/or to reduce strain on the engine.