A recent and quite promising technique for bone tissue engineering is the 3D printing, peculiarly regarding the production of high-quality scaffolds. The 3D printed scaffold strictly provides suitable characteristics for living cells, in order to induce treatment, reconstruction and substitution of injured tissue. The purpose of this work was to evaluate the behavior of the 3D scaffold based on Poly(L-co-D,L lactic acid-co-Trimethylene Carbonate) (PLDLA-TMC), which was designed in Solidworks™ software, projected in 3D Slicer™, 3D printed in filament extrusion, cultured with mesenchymal stem cells (MSCs) and tested in vitro and in vivo models. For in vitro study, the MSCs were seeded in a PLDLA-TMC 3D scaffold with 600 μm pore size and submitted to proliferation and osteogenic differentiation. The in vivo assays implanted the PLDLA-TMC scaffolds with or without MSCs in the calvaria of Wistar rats submitted to 8 mm cranial bone defect, in periods of 8–12 weeks. The results showed that PLDLA-TMC 3D scaffolds favored adherence and cell growth, and suggests an osteoinductive activity, which means that the material itself augmented cellular differentiation. The implanted PLDLA-TMC containing MSCs, showed better results after 12 weeks prior grafting, due the absence of inflammatory processes, enlarged regeneration of bone tissue and facilitated angiogenesis. Notwithstanding, the 3D PLDLA-TMC itself implanted enriched tissue repair; the addition of cells known to upregulate tissue healing reinforce the perspectives for the PLDLA-TMC applications in the field of bone tissue engineering in clinical trials.