In the last decade, the friction stir welding of polymers has been increasingly investigated by the means of more and more sophisticated approaches. Since the early studies, which were aimed at proving the feasibility of the process for polymers and identifying suitable processing windows, great improvements have been achieved. This owes to the increasing care of academic researchers and industrial demands. These improvements have their roots in the promising results from pioneer studies; however, they are also the fruits of the adoption of more comprehensive approaches and the multidisciplinary analyses of results. The introduction of instrumented machines has enabled the online measurement of processing loads and temperature, and critical understanding of the principal aspects affecting the material flow and welds quality. Such improvements are also clearly demonstrated by the increase of the strength of recent joints (up to 99% of joining efficiency) as compared to those reached in early researches (almost 47%). This article provides a comprehensive review of the recent progresses on the process fundamentals, quality assessment and the influence of process parameters on the mechanical behavior. In addition, emphasis is given to new developments and future perspectives.