A firm connection of the bone-implant-fixation system is of utmost importance for patients with cranial defects. In order to improve the connection reliability, the current research focuses on finding the optimal fixation method, as well as selection of the implant manufacturing methods and the used materials. For the latter, implementation of bioactive materials such as hydroxyapatite or other calcium phosphates has also been considered in the literature. The aim of this study was to investigate the effect of gradual osseointegration on the biomechanical performance of cranial Ti6Al4V implants with a deposited HA coating as the osseointegration agent. This effect was assessed by two different computational approaches using finite element method (FEM) modeling. The values of key input parameters necessary for FEM were obtained from experimental plasma spray deposition of HA layers onto Ti6Al4V samples. Immediately upon implantation, the HA layer at the bone-implant contact area brought only a slight decrease in the values of von Mises stress in the implant and the micro-screws when compared to a non-coated counterpart; importantly, this was without any negative trade-off in other important characteristics. The major benefit of the HA coatings was manifested upon the modeled osseointegration: the results of both approaches confirmed a significant reduction of investigated parameters such as the total implant displacements (reduced from 0.050 mm to 0.012 mm and 0.002 mm while using Approach I and II, respectively) and stresses (reduced from 52 MPa to 10 MPa and 1 MPa) in the implanted components in comparison to non-coated variant. This is a very promising result for potential use of thermally sprayed HA coatings for cranial implants.