The present invention provides a friction stir welding apparatus and associated thermal management systems and methods for joining one or more similar or dissimilar materials forming a workpiece along a joint to be welded. The friction stir welding apparatus includes a pin tool apparatus selectively disposed adjacent to and in direct contact with a first surface of the workpiece along the joint to be welded and a heating member disposed adjacent to a second surface of the workpiece along the joint to be welded, the heating member operable for controllably heating at least a portion of the workpiece adjacent to the joint to be welded. The friction stir welding apparatus also includes an annular spindle having an interior portion and an axis, the interior portion of the annular spindle at least partially defining one or more cooling channels, the one or more cooling channels operable for containing a cooling fluid. The friction stir welding apparatus further includes a shoulder disposed adjacent to the annular spindle and substantially aligned with the axis of the annular spindle and a pin tool disposed adjacent to the shoulder and substantially aligned with the axis of the annular spindle. The cooling fluid is operable for cooling at least one of the shoulder and the pin tool.