Polyetheretherketone (PEEK) is a novel polymer material with excellent material properties. The hardness and strength of PEEK can be further improved by introducing fiber reinforcements to meet the high-performance index of the aerospace industry. The machinability will be influenced when the material properties change. Therefore, it is crucial to investigate the influence of material properties of the fiber-reinforced PEEK on machinability. In this paper, the main materials include pure PEEK, short carbon-fiber-reinforced PEEK (CF/PEEK), and short glass-fiber-reinforced PEEK (GF/PEEK). The effects of the fiber type and mass fraction on the tensile strength, hardness, and elastic modulus of materials were discussed using the tensile test and nanoindentation experiments. Furthermore, the fiber-reinforced PEEK lapping machinability was investigated using lapping experiments with abrasive papers of different mesh sizes. The results showed that the hardness and elastic modulus of PEEK could be improved with fiber mass fraction, and the tensile strength of CF/PEEK can be improved compared with that of GF/PEEK. In terms of lapping ability, the material removal rates of the fiber-reinforced materials were found to be lower than the pure PEEK due to the higher hardness of the fiber. During the lapping process, the material removal methods mainly included the ductile deformation or desquamation of reinforcing fiber and ductile removal of the PEEK matrix. The lapped surface roughness of PEEK material can be improved by fiber reinforcement.