The present invention relates to a fuel cell system for vehicles and a method for controlling the same which stably maintains an output of a fuel cell by precisely estimating a recirculated hydrogen amount to a stack. A fuel cell system according to the present invention may include: a stack comprising a plurality of unit cells for generating electrical energy by electrochemical reaction of a fuel and an oxidizing agent; a blower for recirculating a gas exhausted from the stack so as to supply the gas back to the stack; an ejector for recirculating the gas exhausted from the stack, receiving hydrogen so as to mix the hydrogen to the recirculated gas, and supplying the mixture to the stack; a sensor module for detecting a driving condition of the vehicle; and a control portion for controlling operations of the blower and the ejector by using the driving condition of the vehicle and performance maps of the blower and the ejector.