Controlling the tribological performance of fused filament fabrication (FFF) components remains a challenge, which depends on the understanding of their wear mechanisms. In this study, the effects of deposition strategies (Top, Front, and Side, corresponding to sliding surfaces perpendicular to the building, transverse, and scanning directions, respectively) and annealing temperatures (200 degrees C, 250 degrees C, and 300 degrees C) on the anisotropic tribological performance of FFF-printed polyether ether ketone (PEEK) and short carbon fiber-reinforced PEEK (CFR-PEEK) were investigated. We used a 316 L stainless steel ball as the counterpart for reciprocating sliding wear tests under water-lubricated conditions, detailing how the shift in the wear mechanism is attributed to the combined effect of the interfacial weld strength of the deposited layers, the fiber-matrix bonding strength, and the matrix crystallinity. The results show that the specific combination of deposition strategy and annealing temperature can effectively improve the wear performance of FFF-PEEK composites. For CFR-PEEK, the wear performance of Top specimens was best at the annealing temperature of 200 degrees C, Front specimens at 300 degrees C, and Side specimens were unsatisfactory at all annealing temperatures. Furthermore, fiber orientation is the predominant factor in determining the anisotropic tribological performance of CFR-PEEK, but the effect of the deposited layer orientation on the anisotropy should not be neglected. The findings offer critical insights for optimizing the design and fabrication of FFF-PEEK components for tribological applications.