Cranial implants are used to secure intracranial structures, reconstruct the skull contour, normalise cerebral haemodynamic and repair cranial defects. Larger bone defects require intervention for repair from an implant made from autologous bone or other material. To repair such defects using implants, materials necessitate biocompatibility with the natural bone. Patient-specific implants are designed to repair specific cranial defects following standard procedures for implant design, fabrication and cranioplasty. Autologous bone, bone cement comprising hydroxyapatite, polymethyl methacrylate, medical-grade titanium alloy (Ti-6Al-4V) and polyether-ether-ketone, are widely used to fabricate patient-specific implant for repairing different types of bone defects. To optimize a patient-specific implant for shape, size and weight, it is essential to design the implant using 3D modelling and fabrication techniques. Effective attachment of an implant material with a defective skull is also influenced by the joints and fixture arrangements at the interface, these fixtures can be of various types, and materials have different joining procedures. In this study, a comparative analysis of different cranial implant materials (autologous bone, PMMA, polyether-ether-ketone and Ti-6Al-4V) attached to a defective skull with Ti-6Al-4V and polyether-ether-ketone fixture plates has been performed, using finite element analysis. Two types of fixture designs were used as square ‘X’ and linear shapes, which were fixed along with the interface between the implant and the skull. Four fixture plates were fixed symmetrically along the boundary to maximising stability. The findings suggested that all the implant materials were able to sustain extreme boundary conditions such as external loads of 1780 N and intracranial pressure of 15 mmHg without failures. Polyether-ether-ketone implants exhibited 13.5–35% lower von Mises stresses in comparison to autologous bone implants and the square ‘X’ fixture design provided higher stress-relieving results in comparison to Linear fixtures by nearly 18.4% for Ti-6Al-4V fixture material and 10.9% for polyether-ether-ketone fixture material, thereby, encouraging polyether-ether-ketone as an alternative to conventional cranial implant and fixture materials.