CF-PEEK composites were manufactured by 3D-printing using a novel FDM methodology and customized printer and were compared with their cast counterparts. The characterization of composite thermal properties in the range 25–300 °C revealed that 3D-printed CF-PEEK composites manifest 25–30% lower thermal conductivity than cast composites. Short carbon fibers used for reinforcement showed orientation along the polymer flow both in cast and 3-D printed samples causing the anisotropy of thermal properties. The hierarchical nature of 3DP CF-PEEK porosity was observed by SEM imaging, which allowed the identification of large scale inter-layer gaps and cracks, and fine scale intra-layer defects that are likely to be induced by the thermal and mechanical gradients within the deposit that arise during fabrication. Purposeful lay-up of long continuous carbon yarns during 3D-printing opens a way to fabricate tailored mechanical parts with desired anisotropy of properties.