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Abstract Background Critical-sized bone defects, mainly from trauma, infection or tumor resection are a challenging condition, often resulting in prolonged, complicated course of treatment. Autografts are considered as the gold standard to replace lost bone. However, limited amount of bone graft volume and donor-site morbidity have established the need for the development of alternative methods such as scaffold-based tissue engineering (TE). The emerging market of additive manufacturing (3D-printing) has markedly influenced the manufacturing of scaffolds out of a variety of biodegradable materials. Particularly medical-grade polycaprolactone and tricalcium phosphate (mPCL–TCP) scaffolds show appropriate biocompatibility and osteoconduction with good biomechanical strength in large preclinical animal models. This case report aims to show first evidence of the feasibility, safety, and efficacy of mPCL–TCP scaffolds applied in a patient with a long bone segmental defect. Case presentation The presented case comprises a 29-year-old patient who has suffered a left-sided II° open femoral shaft fracture. After initial external fixation and subsequent conversion to reamed antegrade femoral nailing, the patient presented with an infection in the area of the formerly open fracture. Multiple revision surgeries followed to eradicate microbial colonization and attempt to achieve bone healing. However, 18 months after the index event, still insufficient diaphyseal bone formation was observed with circumferential bony defect measuring 6 cm at the medial and 11 cm at the lateral aspect of the femur. Therefore, the patient received a patient-specific mPCL–TCP scaffold, fitting the exact anatomical defect and the inserted nail, combined with autologous bone graft (ABG) harvested with the Reamer–Irrigator–Aspirator system (RIA—Synthes®) as well as bone morphogenetic protein-2 (BMP-2). Radiographic follow-up 12 months after implantation of the TE scaffold shows advanced bony fusion and bone formation inside and outside the fully interconnected scaffold architecture. Conclusion This case report shows a promising translation of scaffold-based TE from bench to bedside. Preliminary evidence indicates that the use of medical-grade scaffolds is safe and has the potential to improve bone healing. Further, its synergistic effects when combined with ABG and BMP-2 show the potential of mPCL–TCP scaffolds to support new bone formation in segmental long bone defects.