The mechanical properties of hydroxyapatite related macroporous biocomposites (MPBs) are influenced by a number of factors, such as the pore size, the filler content and the properties of the matrix and the inclusion. Failure often occurs when the strength of the implant cannot bear the applied mechanical load. In this study, the effects of filler content on the mechanical properties of MPBs have been investigated. A finite element (FE) unit cell model of a macroporous hydroxyapatite-polyetheretherketone (HA-PEEK) biocomposite structure with uniform and interconnected pores has been constructed. In the FE model, the HA particles were assumed to have random distribution, and particle volume fraction would be varied in the PEEK matrix. The material behaviours of both HA and PEEK have been implemented in the ABAQUS finite element code. HA was modelled to exhibit elastic behaviour and undergo plastic softening to a residual strength when a critical stress was reached, while the PEEK matrix would follow elastic-plastic behaviour. The macroscopic compressive stress-strain relations of the macroporous biocomposite structures have been predicted. Increasing particle volume fraction could lead to an increase in the compressive elastic modulus of the structures but a reduction in the compressive strength. The von Mises stress distribution and the effect of stress concentration in the structures with different filler content are also discussed. The proposed model could provide macro-structural and microscopic information of the macroporous biocomposite structure to the designers in order to facilitate the fabrication of this kind of structure with optimum mechanical properties.