A method for controlling a fuel pressure valve of a vehicle may include stop entrance, of reducing a target fuel pressure below a predetermined value based on an engine RPM and increasing an allowable deviation between the target fuel pressure and an actual fuel pressure measured by a sensor when a controller determines that a current vehicle speed is equal to or lower than a reference vehicle speed, and pressing of an acceleration pedal is released, fuel pressure determination, of determining whether a deviation value between the target fuel pressure and the measured actual fuel pressure is greater than the allowable deviation, and valve control, of determining a duty value of the fuel pressure valve when the deviation value between the target fuel pressure and the measured actual fuel pressure is greater than the allowable deviation, and then controlling to open the fuel pressure valve using the determined duty value.