The weldability of 3D printed (3DP), through material extrusion (MEX), of Polyamide 6 (PA6) plates joined with FSW is investigated. FSW has its challenges in polymers, especially for 3D printed parts, while it is used for various industrial applications in the automotive and airspace sector, in joints, and in other types of parts. Herein, a full factorial experimental course was deployed, to quantitatively document the impact of three critical process parameters (e.g., the rotational speed and the travel speed of the tool, as well as the pin geometry of the tool) and to optimize their levels. A set of identical PA6 prismatic workpieces was prepared and then welded. Throughout the welding process, the temperature profiles were monitored and logged, to ensure the solid state of the workpiece material. The welding efficiency of the joints was then determined through mechanical tests, while unwelded 3D printed specimens were employed as control samples. Thorough morphological evaluations and characterization with microscopy (Scanning Electron and optical Microscopy) were performed for the welding zones. The evaluation of the metrics with statistical modeling tools led to the quantitative correlation of the process parameters, as well as their interactions, and finally optimization. The feasibility of joining 3DP PA6 with FSW was verified, reaching a welding efficiency of up to 120.40% for threaded cylindrical pin profile, rotational speed 1200 rpm, and travel speed 3 mm/min. The results of the study provide valuable information and merit for the FSW of 3DP PA6, which can be exploited in various industrial applications.