Polyetheretherketone (PEEK) has emerged as the material of choice for spinal fusion devices, replacing conventional materials such as titanium and its alloys due to its ability to easily overcome a lot of the limitations of traditional metallic biomaterials. However, one of the major drawbacks of this material is that it is not osteoinductive, nor osteoconductive, preventing direct bone apposition. One way to overcome this is through the modification of the PEEK with bioactive calcium phosphate (CaP) materials, such as hydroxyapatite (HA–Ca10(PO4)6(OH)2). RF magnetron sputtering has been shown to be a particularly useful technique for the deposition of CaP coatings due to the ability of the technique to provide greater control of the coating’s properties. The work undertaken here involved the deposition of HA directly onto PEEK via RF magnetron at a range of deposition times between 10–600 min to provide more bioactive surfaces. The surfaces produced have been extensively characterised using X-Ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscopy (SEM), stylus profilometry, and Time of Flight Secondary Ion Mass Spectrometry (ToFSIMS). XPS results indicated that both Ca and P had successfully deposited onto the surface, albeit with low Ca/P ratios of around 0.85. ToFSIMS analysis indicated that Ca and P had been homogeneously deposited across all the surfaces. The SEM results showed that the CaP surfaces produced were a porous micro-/nano-structured lattice network and that the deposition rate influenced the pore area, pore diameter and number of pores. Depth profiling, using ToFSIMS, highlighted that Ca and P were embedded into the PEEK matrix up to a depth of around 1.21 µm and that the interface between the CaP surface and PEEK substrate was an intermixed layer. In summary, the results highlighted that RF magnetron sputtering can deliver homogenous CaP lattice-like surfaces onto PEEK in a direct, one-step process, without the need for any interlayers, and provides a basis for enhancing the potential bioactivity of PEEK.