The structural integrity of 3D-printed cement composites is critical for their widespread application in construction, where anisotropic mechanical properties pose challenges for load bearing applications. This paper investigates the anisotropic behavior of carbon nanotubes (CNTs) and silica fume integrated into 3D-printed cementitious materials. The flexural strengths after 7 days of curing were determined for 3D-printed specimens by varying directions of loading, i.e., perpendicular and parallel to the plane of printed layers for mixes containing CNTs and silica fume individually. The flexural strength was higher when the load was applied parallel to the printing direction for all mixtures due to stronger bonding and load distribution of 3D-printed structures. Conversely, the strength was restricted by weakened inter-layer bonding when the load was applied perpendicular to the printing direction. For instance, a mixture containing 5% silica fume showed a 24% higher flexural strength when burden was parallel to the printing direction compared to perpendicular orientation. Conversely, mixture containing 0.2% CNTs showed an increment of 11.6% under the same conditions. Moreover, the addition of 0.2% CNTs improved the flexural strength by 106% compared to a mix containing silica fume when the load was applied perpendicular to the printing direction. Therefore, incorporating CNTs strengthened the layer interface and reduced the variation in flexural strength between the two loading orientations, thereby enhancing inter-layer bonding of 3D-printed structures.