Polyetheretherketone (PEEK) is a promising biomaterial due to its excellent mechanical properties. Most PPEK manufacturing methods include additive manufacturing, injection molding, grinding, pulse laser drilling, or incremental sheet forming. Rotary friction welding (RFW) is a promising bonding technique in many industries. However, very few studies have focused on the RFW of PEEK. Conventionally, the number of revolutions is fixed during the welding process. Remarkably, the rotary friction welding of PEEK polymer rods using an innovative variable rotational speed is investigated in this study. The average bending strength of the welded part using a three-stage transformation rotational speed was enhanced by about 140% compared with a rotational speed of 1000 rpm. The advantage of computer numerical controlled RFW of PEEK using variable rotational speed is a reduced cycle time of RFW. A reduction in cycle time of about 6% can be obtained using the proposed RFW with a three-stage transformation rotational speed. The innovative approach provides low environmental pollution and high energy efficiency and complies with sustainable development goals.