An apparatus and a method for inspecting navigation safety facilities by using a flight vehicle are disclosed. The method for inspecting navigation safety facilities by using a flight vehicle comprises the steps of: defining a three-dimensional flight path for a flight vehicle so that same passes through navigational safety facilities; receiving a navigation signal value from the navigation safety facilities and GPS data of the flight vehicle, the navigation signal value and the GPS data being measured by the flight vehicle automatically flying along the defined three-dimensional flight path; analyzing the navigation signal value so as to estimate the distance and the angle of the flight vehicle viewed from the navigation safety facilities; and inspecting the navigation safety facilities according to whether the coordinates of the flight vehicle identified by the GPS data are included in an area formed by the distance and the angle.