As a rapidly developing additive manufacturing technology, fused deposition modeling (FDM) has become widespread in many industry fields. It can fabricate complicated geometries using filament of thermoplastic materials such as PP, polylactic acid, acrylonitrile butadiene styrene, etc. However, poor mechanical properties of raw materials limit their application. Poly-ether-ether-ketone is a type of special engineering plastic with high performance, which could be further reinforced by adding carbon fibers (CFs). During FDM process, the mechanical properties of printed parts are largely subject to careful selection of process parameters. To improve the mechanical properties of PEEK and CF/PEEK 3D-printed parts, the effects of various process parameters including building orientation, raster angle, nozzle temperature, platform temperature, ambient temperature, printing speed, layer thickness, infill density, and number of printed parts on mechanical properties were investigated. The tensile fracture interfaces of printed parts were observed by scanning electron microscope (SEM) to explain the influence mechanism of process parameters. In the single factor experiments, flat and on-edge specimens show the best tensile and flexural strength, respectively; the specimens with raster angle ±45° and 0° show the best tensile and flexural strength, respectively. When the nozzle temperature at 500°C, platform temperature at 200°C, ambient temperature at 150°C, printing speed is 20 mm/s, layer thickness is 0.2 mm, and infill density is 100%, the printed parts exhibit the best mechanical properties.