Cranioplasties show overall high complication rates of up to 45.3%. Risk factors potentially associated with the occurrence of postoperative complications are frequently discussed in existing research. The present study examines the positioning of 39 patient-specific implants (PSI) made from polyetheretherketone (PEEK) and retrospectively investigates the relationship between the fitting accuracy and incidence of postoperative complications. To analyze the fitting accuracy of the implants pre- and post-operatively, STL files were created and superimposed in a 3D coordinate system, and the deviations were graphically displayed and evaluated along with the postoperative complications. On average, 95.17% (SD = 9.42) of the measurements between planned and surgically achieved implant position were within the defined tolerance range. In cases with lower accordance, an increased occurrence of complications could not be demonstrated. The overall postoperative complication rate was 64.1%. The fitting of the PEEK-PSI was highly satisfactory. There were predominantly minor deviations of the achieved compared to the planned implant positions; however, estimations were within the defined tolerance range. Despite the overall high accuracy of fitting, a considerable complication rate was found. To optimize the surgical outcome, the focus should instead be directed towards the investigation of other risk factors.