Friction Stir Welding (FSW) is a solid state joining process primarily meant for joining metals and its alloys is also used in the joining of polymers. Researchers have carried out FSW on different thermoplastics. However, the joining of Polyether ether ketone (PEEK), a thermoplastic material with high strength and high temperature resistance used in aerospace, automotive, chemical processing industries and medical applications has not been carried out extensively using FSW. PEEK is a semi-crystalline polymer having a glass transition temperature of 143 degrees C, melting point of 343 degrees C and tensile strength around 100 MPa. This research paper is aimed at joining of PEEK plates by FSW process with different tool rotating speeds (500, 710, 1000 rpm) and welding feed rates (16, 20, 31.5 mm/min) as input process parameters. FSW process is carried out by modifying the milling machine with a specially made suitable fixture for holding the two work materials to be welded. PEEK material (100% virgin) of 5.5 mm thickness is used as the workpiece for the joining process. Experiments are conducted using a mild steel cylindrical tool of 20 mm tool shoulder diameter, 6 mm probe pin diameter and 5 mm probe pin length. The FSW butt joints of PEEK plates are fabricated, characterized and analysed. The study on tensile strength reveals that the strength decreases with increase in tool rotating speed and welding feed rate. The ANOVA results predict that both the tool rotating speeds and welding feed rates are significant parameters. Also hardness is higher on the advancing side of the joint than the retreating side of the joint. The SEM macrograph shows the different zones of FSW processed joints and the mechanism of FSW welded joint is investigated detailed in this paper. (C) 2020 Elsevier Ltd. All rights reserved.