Three-dimensional printed polycaprolactone/β-tricalcium phosphate (PCL/β-TCP) scaffolds reinforced with carbon nanotubes (CNTs) were fabricated and characterized for bone tissue engineering applications. The incorporation of CNTs significantly enhanced the mechanical properties, with the aligned PCL/β-TCP/CNT scaffold (1 wt% CNTs) exhibiting a 125% and 123% increase in compressive modulus (180.3 ± 10.1 MPa) and strength (7.8 ± 0.6 MPa), respectively, compared to the PCL/β-TCP scaffold. The β-glycerol phosphate (BGP)-modified PCL/β-TCP/CNT scaffold showed similar mechanical properties to the aligned scaffold. All scaffolds maintained high porosity (> 70%) and a wide pore size distribution (50–500 μm). The scaffolds demonstrated excellent biocompatibility, with hemolysis rates below 5% and high cell viability. The aligned PCL/β-TCP/ CNT scaffold promoted the highest rat adipose-derived stem cell proliferation, while the BGP-modified scaffold enhanced human dental pulp stem cell proliferation and mineralization.