Despite the widespread use of fused filament fabrication (FFF) (an extrusion-based additive manufacturing process) to manufacture end-use parts for the aerospace industry, limited materials are available within this process that can be used for structural applications in the harsh space environment. Currently available high-performance polymers need to be improved by incorporating additives within the polymer matrix to achieve multi-functional properties. Additives such as graphene, graphene oxide, carbon nanotubes and boron carbide are known to improve mechanical and thermal properties and radiation shielding. This study aims to understand if these additives can be successfully incorporated into PEKK matrix to manufacture printable filaments for FFF. Graphene, graphene oxide (GO) and boron carbide (B4C) were compatibilised with PEKK matrix, and their mechanical, thermal and rheological properties were analysed and compared with commercially available carbon fibre and carbon nanotube-reinforced PEKK where appropriate. As rheological properties of the formulations confirmed that they were printable, filaments for FFF were then manufactured. Graphene–PEKK was the most printable filament followed by GO–PEKK while B4C–PEKK was not printable. TEM images of filament cross-section showed good dispersion of graphene and graphene oxide, while boron carbide formed large agglomerates; B4C also presented feeding issues due to its hardness which affected its printability. Dispersion of the additives was also confirmed by studying their X-ray diffraction (XRD) patterns, and chemical structures were assessed using FT-IR spectroscopy. Finally, parts were printed using selected composite filaments, and their porosity and surface roughness were compared with neat PEKK and commercial CNT-reinforced PEKK to develop an understanding of metrology and bulk material properties of the composites.