Nanocomposite scaffolds with tailored 3D pore configuration are promising candidates for the reconstruction of bone. Here we fabricated novel nanocomposite bone scaffolds through robocasting. Poly(caprolactone) (PCL)-hydroxyapatite (HA) slurry containing ionically modified carbon nanotubes (imCNTs) was robotic-dispensed and structured layer-by-layer into macrochanneled 3D scaffolds under adjusted processing conditions. Homogeneous dispersion of imCNTs (0.2 wt % relative to PCL-HA) was achieved in acetone, aiding in the preparation of PCL-HA-imCNTs slurry with good mixing property. Incorporation of imCNTs into PCL-HA composition significantly improved the compressive strength and elastic modulus of the robotic-dispensed scaffolds (~1.5-fold in strength and ~2.5-fold in elastic modulus). When incubated in simulated body fluid (SBF), PCL-HA-imCNT nanocomposite scaffold induced substantial mineralization of apatite in a similar manner to the PCL-HA scaffold, which was contrasted in pure PCL scaffold. MC3T3-E1 cell culture on the scaffolds demonstrated that cell proliferation levels were significantly higher in both PCL-HA-imCNT and PCL-HA than in pure PCL, and no significant difference was found between the nanocomposite scaffolds. When the PCL-HA-imCNT scaffold was implanted into a rat subcutaneous tissue for 4 weeks, soft fibrous tissues with neo-blood vessels formed well in the pore channels of the scaffolds without any significant inflammatory signs. Tissue reactions in PCL-HA-imCNT scaffold were similar to those in PCL-HA scaffold, suggesting incorporated imCNT did not negate the beneficial biological roles of HA. While more long-term in vivo research in bone defect models is needed to confirm clinical availability, our results suggest robotic-dispensed PCL-HA-imCNT nanocomposite scaffolds can be considered promising new candidate matrices for bone regeneration.