Thermoplastic parts fabricated by material extrusion (MEX) 3D printing usually possess weak inter-layer bonding, leading to low mechanical performance in the Z-direction. Here, we develop a simple but effective post-treatment method to improve the Z-strength of MEX-printed acrylonitrile butadiene styrene (ABS) parts. In this method, commercial carbon fiber (CF) tows and epoxy were embedded into internal channels in MEX-printed structures to form high-strength CF/epoxy pins. Due to the mechanical interlock between the CF/epoxy pins and the printed ABS, the Z-strength of the printed parts improved significantly. Specifically, the Z-pinned ABS samples exhibit a strength of up to 71.74 MPa and a Young’s modulus of up to 5.93 GPa in the transverse direction, which were 335 % and 266 % higher than those of the printed neat counterparts, respectively. We find that the mechanical performance of the Z-pinned samples follows a simple rule of mixtures which is able to capture the Z-dependent mechanical strength and Young’s modulus. Also, curved CF/epoxy pins were successfully formed within printed thin-walled curved structures, offering the capability to strengthen MEX printed structures with complex shapes. This work demonstrates that the Z-pin embedding process can be an effective approach to improve the transverse strength of the MEX printed parts for load-bearing structural applications.