Fish bone extract (FBE) containing a trioligopeptide (FBP-KSA, Lys-Ser-Ala) isolated from Johnius belengerii could induce osteogenic activities on MC3T3-E1 pre-osteoblasts in our previous study. Regarding the osteogenic effect of FBE, in the present study, we fabricated the three-dimensional (3D) interconnected polycaprolactone (PCL)/FBE scaffolds for bone tissue regeneration. After fabrication of PCL scaffolds using 3D printing, FBE was coated on the surface of PCL scaffolds by self-assembly process. In the physical characteristic and mechanical property tests, the results demonstrated that the fabricated scaffolds have the strut diameter (between 340 and 345 μm), pore size (between 470 and 480 μm), porosity (between 50% and 55%), and tensile properties (Young's modulus: 9.18-9.42 MPa; max tensile strengths 82.3-87.4 MPa) were similar to those of PCL scaffold. In the cell proliferation and osteogenic assay, the results showed that PCL/FBE scaffolds could significantly induce cell proliferation, calcium deposition, and the expression of osteogenic phenotype markers such as alkaline phosphatase, osteopontin, osteocalcin, and bone morphogenetic protein-2 in the osteoblasts. These results suggest that FBE-coated PCL scaffolds are promising materials for use in biomedical application to promote bone tissue regeneration.