Short-carbon-fiber (SCF)–reinforced poly-ether-ether-ketone (PEEK) is a promising polymer composite material with good biocompatibility, a high strength-to-weight ratio, and low friction properties. In artificial-bone fabrication and other applications with more flexible fabrication demands, fused-deposition modeling (FDM) technology enables the rapid and low-cost fabrication of SCF/PEEK parts with sophisticated structures. Owing to the high viscosity of melting PEEK composites, great challenges, associated with the poor internal interface, need to be overcome before enhanced mechanical properties can be obtained. In this study, key processing parameters and various SCF amounts were studied to investigate their effects on the mechanical properties of PEEK composites. It was revealed that the existence of voids and gaps between the SCF and PEEK led to a decrease in the strength of the composite systems. The FDM processing parameters were tuned to eliminate these defects in the PEEK composites. The tensile strength of the 2% SCF/PEEK sample reached 96.4 MPa, which is comparable to that of PEEK parts prepared by injection molding. Meanwhile, its elastic modulus reached 2.6 GPa, which is 169% higher than that of the bare PEEK sample.