A friction stir welding apparatus and a method of operating the friction stir welding apparatus are disclosed. The friction stir welding apparatus includes a rotary tool whose extremity constitutes a probe, a retaining arm which supports the rotary tool, and a roller provided at a position of the retaining arm opposite the rotary tool. The method includes adjusting the retaining arm so as to position workpieces between the rotary tool and the roller while adjusting the roller to turn in a direction where a joint line of the workpieces extends, rotating the rotary tool and lowering the probe until the probe presses the workpieces, gradually inserting the probe into the joint line, and moving the probe along the joint line.