Several types of three-dimensional (3D)-printed tracheal scaffolds have been reported. Nonetheless, most of these studies concentrated only on application of the final product to an in vivo animal study and could not show the effects of various 3D printing methods, materials, or parameters for creation of an optimal 3D-printed tracheal scaffold. The purpose of this study was to characterize polycaprolactone (PCL) tracheal scaffolds 3D-printed by the 4-axis fused deposition modeling (FDM) method and determine the differences in the scaffold depending on the additive manufacturing method. The standard 3D trachea model for FDM was applied to a 4-axis FDM scaffold and conventional FDM scaffold. The scaffold morphology, mechanical properties, porosity, and cytotoxicity were evaluated. Scaffolds were implanted into a 7 × 10-mm artificial tracheal defect in rabbits. Four and 8weeks after the operation, the reconstructed sites were evaluated by bronchoscopic, radiological, and histological analyses. The 4-axis FDM provided greater dimensional accuracy and was significantly closer to CAD software-based designs with a predefined pore size and pore interconnectivity as compared to the conventional scaffold. The 4-axis tracheal scaffold showed superior mechanical properties. We suggest that the 4-axis FDM process is more suitable for the development of an accurate and mechanically superior trachea scaffold.