The joining tool according to the present invention is provided with a rotor and a probe having a diameter smaller than a diameter of the rotor. The probe is protruded from a part of an end face of the rotor. A groove is formed at least on a middle portion of a peripheral surface of the probe so as to extend in the axial direction of the probe. The probe is provided with an agitating protrusion formed only on a region of from the basal end portion of the probe to a longitudinal middle portion. In a friction agitation joining method according to the present invention, the rotating probe of the aforementioned joining tool inserted into stacked joining members such that the groove crosses a superposed interface between the joining members and that the protrusion is buried only in one of the joining members located at a probe basal end side. While keeping this state, the probe is moved relative to the joining members to thereby join the joining members.