The fuel pump control system includes an electronic control unit (ECU) for controlling the discharge capacity of a plunger type high pressure fuel pump driven by a driving cam connected to the camshaft of an engine. The engine is provided with a variable valve timing device for controlling valve timing of the engine by adjusting the rotation phase of the camshaft relative to the crankshaft. The pump is provided with a suction valve. When the open/close timing of the suction valve changes, the effective discharge stroke of the pump and, thereby the discharge capacity of the pump changes. The ECU estimates the change in the valve timing of the engine during the effective discharge stroke of the pump before the effective discharge stroke starts, and adjusts the open/close timing of the suction valve in accordance with the estimated change in the valve timing so that the discharge capacity of the pump becomes a target discharge capacity regardless of the change in the valve timing of the engine.