A coolant temperature controller for a fuel cell vehicle comprises: a housing including first and second inlet ports provided on one side thereof and an exhaust port provided on the other side thereof in a horizontal direction with respect to the first inlet port; a plunger operating portion including an operating plunger for capable of vertical movement between the first and second inlet ports and the exhaust port of the housing to proportionally control degree of opening of the first and second inlet ports; a motor mounted on the top of the plunger operating portion; and a motor shaft connected to the motor and extending from the motor to the bottom of the plunger operating portion to be connected to the operating plunger, wherein the vertical movement of the operating plunger is driven by a rotational force transmitted through the motor shaft as the motor operates. The controller can maintain the coolant at a preset temperature for optimal operation of the fuel cell stack.