Interest in proton therapy has increased in the last decade, as protons are effective to treat deeply located tumors, cause less damage to healthy tissue and allow controlling the energy to be transferred in a target-oriented manner (or energy transfer within target limits). It is known that secondary particles such as neutrons are produced by a result of nuclear interactions of protons with the target. Secondary neutrons can cause an uncontrolled dose increase in healthy tissue near the target site, and because they have a high radiobiological effectiveness, they raise the risk of secondary cancer. There are not enough studies examining the effect of biomaterials on secondary neutron production (SNP) in proton therapy. This study aims to investigate the effect of biomaterials used as implants instead of cranium in the skull on proton depth dose distribution and SNP with Monte Carlo-based PHITS code. Therefore, Bragg peaks and SNPs for 40–140 MeV energy protons were calculated and compared with the literature in a slab head phantom containing stainless steel, CoCrMo (CCM) alloy, alumina, polytetrafluoroethylene, Ti alloy, and NiTi alloy biomaterials used in cranioplasty. It was observed that the most compatible biomaterial compared to cranium for all energies is polytetrafluoroethylene. When polytetrafluoroethylene biomaterial was placed instead of the cranium in the skull, the Bragg peak position of the 100 MeV protons was decreased by 5.04% compared to that in the cranium. In this case, the energy absorbed in the polytetrafluoroethylene biomaterial increased by approximately 28% compared to the cranium, while it decreased by approx. 4% in the brain tissue. It was also observed that while SNP was 0.0501 in the cranium, it increased by almost 18% in PTFE.