Polyether-ether-ketone (PEEK) is believed to be the next-generation biomedical material for orthopaedic implants that may replace metal materials because of its good biocompatibility, appropriate mechanical properties and radiolucency. Currently, some PEEK implants have been used successfully for many years. However, there is no customised PEEK orthopaedic implant made by additive manufacturing licensed for the market, although clinical trials have been increasingly reported. In this review article, design criteria, including geometric matching, functional restoration, strength safety, early fixation, long-term stability and manufacturing capability, are summarised, focusing on the clinical requirements. An integrated framework of design and manufacturing processes to create customised PEEK implants is presented, and several typical clinical applications such as cranioplasty patches, rib prostheses, mandibular prostheses, scapula prostheses and femoral prostheses are described. The main technical challenge faced by PEEK orthopaedic implants lies in the poor bonding with bone and soft tissue due to its biological inertness, which may be solved by adding bioactive fillers and manufacturing porous architecture. The lack of technical standards is also one of the major factors preventing additive-manufactured customised PEEK orthopaedic implants from clinical translation, and it is good to see that the abundance of standards in the field of additive-manufactured medical devices is helping them enter the clinical market.