An apparatus for injecting a coolant for a fuel cell vehicle is provided. More specifically, a coolant tank stores a coolant and a coolant pump, disposed in a coolant supply line connecting the coolant tank and the stack cooling loop is configured to pressure-transfer the coolant to the stack cooling loop, and circulating the coolant, which has passed through the stack cooling loop, to the coolant tank. A bubble elimination unit, disposed at a rear stage of the coolant pump in the coolant supply line, eliminates the bubbles in the fuel cell stack through vibration. This bubble elimination unit may be configured as an ultrasonic wave excitor for exciting the stack cooling loop with ultrasonic waves.