A method of setting a reference position of an actuator in an automated manual transmission includes: performing Hall signal comparison by comparing, by a controller, a signal value of Hall sensors with a reference signal value; performing first movement by moving, by the controller, a finger of the actuator to a first end in a shifting direction by a preset distance if the signal values are identical; performing a first selection checking by checking whether selecting operation is enabled; performing a second movement by moving the finger to a second end in the shifting direction by a distance that is twice the preset distance if selecting operation is not enabled; performing a second selection checking by checking whether selecting operation is enabled; and performing a third movement by moving the finger to the first end in the shifting direction by the preset distance if selecting operation is not enabled.