The purpose of the following study was to compare the effect of the shape of a tool on the joint and to obtain the values of Friction Stir Welding (FSW) parameters that provide the best possible joint quality. The material used was an aluminium alloy, EN AW-3004 (AlMn1Mg1). To the authors’ best knowledge, no investigations of this alloy during FSW have been presented earlier. Five butt joints were made with a self-developed, cylindrical, and tapered threaded tool with a rotational speed of 475 rpm. In order to compare the welding parameters, two more joints with a rotational speed of 475 rpm and seven joints with a welding speed of 300 mm/min with the use of a cylindrical threaded pin were performed. This involved a visual inspection as well as a tensile strength test of the welded joints. It was observed that the value of the material outflow for the joints made with the cylindrical threaded pin was higher than it was for the joints made with the tapered threaded pin. However, welding defects in the form of voids appeared in the joints made with the tapered threaded tool. The use of the cylindrical tool resulted in higher values for about 37% of mechanical properties compared with the highest result for the tapered threaded joint. As far as the parameters were concerned, it was concluded that most of the specimens were properly joined for a rotational speed of 475 rpm. In the joints made with a welding speed of 300 mm/min, the material was not stirred properly. The best joint quality was given for a rotational speed of 475 rpm as well as a variety of welding speed values between 150 and 475 mm/min.