We developed three-dimensional electrospun silk fibroin (ESF) scaffolds with controllable pore size. The purpose of this study was to evaluate ESF scaffolds with pores (P-ESF) for bone regeneration via in vitro and in vivo studies, with a comparison to a commercially available porous three-dimensional polylactic acid (PLA) scaffold. P-ESF supported significantly higher proliferation and alkaline phosphatase activity of osteoblasts than PLA in vitro (p < 0.05). Moreover, higher expression levels of activated adhesion-related proteins, including focal adhesion kinase, were observed in the P-ESF than in PLA, as confirmed by western blot analyses. Microcomputed tomography revealed that 78.30% of the original bone volume was attained in the P-ESF implantation group at 7 weeks after critical bone defect formation in rat calvaria. Comparatively, the PLA implantation group showed only 49.31%. Histological evaluation also showed new bone tissue formation upon P-ESF implantation. Taken together, the P-ESF scaffold may be a good bone substitute for bone regeneration.