A method and apparatus that compensates for a velocity of a motor of fuel cell vehicle when a resolver is determined to have failed is provided. In particular, a wheel velocity sensor is configured to detect a wheel velocity of a driving wheel, and an ABS controller is configured to calculate an average wheel velocity and transmit the calculated average to a fuel cell controller (FCU). The FCU is configured to receive information related to the wheel velocity upon detecting that the resolver has failed, and control driving of the motor based on the data related to the wheel velocity so that the motor may maintain operation.