As a special engineering polymer, polyether ether ketone (PEEK) has been used widely due to its excellent mechanical properties, high thermal stability, and chemical resistance. Fused deposition modeling (FDM) is a promising process for fabricating PEEK parts. However, due to the semi-crystalline property and high melting point of PEEK, determining appropriate process parameters is important to reduce warpage deformation and improve the mechanical properties of PEEK. In this article, the influence of raster angle and infill density was determined by single factor experiment, which are the two most important parameters. The results showed that samples with 0°/90° raster angle and 50% infill density had the best comprehensive properties in terms of warpage deformation, tensile strength, and specific strength. Subsequently, based on the results above, the effects of printing speed, nozzle temperature, platform temperature, raster width, and layer thickness were analyzed by orthogonal experiment. The results indicated that platform temperature had the greatest impact on warpage deformation while printing speed and nozzle temperature were significant parameters on tensile strength. Through optimization, warpage deformation of the samples could be reduced to almost 0 and tensile strength could increase by 19.6% (from 40.56 to 48.50 MPa). This will support the development of FDM for PEEK.