Background: Bone tissue engineering offers a promising strategy to overcome the limitations of conventional bone grafts, including donor site morbidity and immune rejection. In this study, three-dimensional (3D) polycaprolactone (PCL) scaffolds coated with collagen (Col) were fabricated by extrusion-based printing. The scaffolds were further functionalized with human endometrial mesenchymal stem cells (hEnMSCs) and osteoblast-derived exosomes (ODExo), obtained from osteoblast-like cells, to investigate their potential in bone regeneration. Results: The printed scaffolds exhibited controlled porosity, suitable mechanical integrity, and improved hydrophilicity following collagen coating. ODExo were isolated from osteoblast-like cells and confirmed by morphology and particle size. In vitro analyses revealed that exosome-functionalized scaffolds significantly enhanced cell adhesion, proliferation, and osteogenic differentiation of hEnMSCs, as indicated by increased calcium deposition and elevated expression of osteogenic markers such as alkaline phosphatase, osteocalcin, RUNX2, and osteonectin, even without osteogenic induction medium. In vivo experiments using a rat calvarial defect model demonstrated superior bone formation and matrix mineralization in scaffolds containing exosomes compared with control groups. Moreover, transplantation of PCL/Col scaffolds seeded with hEnMSCs and ODExo implants further promoted bone regeneration in vivo. Conclusions: These findings demonstrate that osteoblast-derived exosomes serve as potent bioactive modulators capable of driving osteogenic differentiation and accelerating bone regeneration. Incorporating exosomes into 3D printed PCL/Col scaffolds provides a promising biomimetic and partially cell-free approach for the treatment of critical-sized bone defects. This strategy highlights the potential of combining advanced scaffold fabrication with bioactive vesicles to improve clinical outcomes in regenerative medicine.