Self-healing and autologous bone graft of calvaraial defects can be challenging. Therefore, the fabrication of scaffolds for its rapid and effective repair is a promising field of research. This paper provided a comparative study on the ability of Three-dimensional (3D) printed polycaprolactone (PCL) scaffolds and PCL-modified with the hydroxyapatite (HA) and bioglasses (BG) bioceramics scaffolds in newly bone formed in calvaria defect area. The studied 3D-printed PCL scaffolds were fabricated by fused deposition layer-by-layer modeling. After the evaluation of cell adhesion on the surface of the scaffolds, they were implanted into a rat calvarial defect model. The rats were divided into four groups with scaffold graft including PCL, PCL/HA, PCL/BG, and PCL/HA/BG and a non-explant control group. The capacity of the 3D-printed scaffolds in calvarial bone regeneration was investigated using micro computed tomography scan, histological and immunohistochemistry analyses. Lastly, the expression levels of several bone related genes as well as the expression of miR-20a and miR-17-5p as positive regulators and miR-125a as a negative regulator in osteogenesis pathways were also investigated. The results of this comparative study have showed that PCL scaffolds with HA and BG bioceramics have a great range of potential applications in the field of calvaria defect treatment.