Bone defects, especially those complicated by infections, pose significant challenges in orthopedic surgery due to their complex healing requirements. This study aimed to develop and evaluate polydopamine (PDA)-modified polycaprolactone/β-tricalcium phosphate (PCL/β-TCP) scaffolds fabricated using 3D printing technology for their osteogenic and antibacterial efficacy. PDA was incorporated at varying concentrations (1%, 3%, and 5%) to enhance the scaffolds' drug-loading capacity and antibacterial properties through vancomycin integration. The scaffolds demonstrated excellent biocompatibility, as confirmed by cell viability, proliferation assays, and histological analyses, supporting osteoblast adhesion and growth. Mechanical testing revealed that PCL/β-TCP/PDA scaffolds exhibited sufficient compressive strength comparable to cancellous bone, with a porous structure facilitating cell infiltration and nutrient exchange. The incorporation of PDA significantly improved drug loading, achieving a vancomycin release duration of up to 144 h, effectively reducing bacterial presence as shown by fluorescence in situ hybridization (FISH) staining. In a rabbit cranial defect model, the PDA concentration does not impede bone regeneration. Micro-CT and immunofluorescence analyses confirmed increased bone formation and the upregulation of osteogenic markers, including ALP, COL-1, and RUNX2. Gene expression analysis highlighted the activation of pathways related to osteoblast differentiation and immune response, further demonstrating the scaffolds' regenerative potential. These findings underscore the dual functionality of PCL/β-TCP/PDA scaffolds in simultaneously addressing bone healing and infection control. The 3D-printed scaffolds offer a promising solution for treating infected bone defects, with potential applications in tissue engineering and regenerative medicine. Further investigations are warranted to optimize long-term drug release kinetics and validate their clinical efficacy.