In an apparatus for controlling an autonomous operating vehicle having a prime mover and operating machine, it is configured to have a geomagnetic sensor responsive to magnets embedded in the area, detect angular velocity generated about z-axis in center of gravity of the vehicle, detect a wheel speed of the driven wheel, store map information including magnet embedded positions, detect a primary reference direction, detect a vehicle position relative to the magnet, and detect a vehicle position in the area, calculate a traveling direction and traveled distance of the vehicle, and control the operation performed through the operating machine in the area in accordance with a preset operation program based on the detected primary reference direction, the detected position of the vehicle in the area, the calculated traveling direction and the calculated traveled distance.