There is an essential clinical need to develop rapid process scaffolds to repair bone defects. The current research presented the development of calcium zirconium silicate/polycaprolactone for bone tissue engineering utilising melt extrusion-based 3D printing. Calcium zirconium silicate (CZS) nanoparticles were added to polycaprolactone (PCL) porous scaffolds to enhance their biological and mechanical properties, while the resulting properties were studied extensively. No significant difference was found in the melting point of the samples, while the crystallisation temperature points of the samples containing bioceramic increased from 36.1 to 40.2 °C. Thermal degradation commenced around 350 °C for all materials. According to our results, increasing the CZS content from 0 to 40 wt.% (PC40) in porous scaffolds (porosity about 55–62%) improved the compressive strength from 2.8 to 10.9 MPa. Furthermore, apatite formation ability in SBF solution increased significantly by enhancing the CZS percentage. According to MTT test results, the viability of MG63 cells improved remarkably (~29%) in PC40 compared to pure PCL. These findings suggest that a 3D-printed PCL/CZS composite scaffold can be fabricated successfully and shows great potential as an implantable material for bone tissue engineering applications.