Congenital diaphragmatic hernia (CDH) is a rare disease in which neonates are born with pulmonary hypoplasia and a diaphragmatic defect. Survival is improving due to advances in fetal intervention for pulmonary hypoplasia leading to increased use of scaffolds for repair. Scaffolds have a significant morbidity rate with recurrence, small bowel obstruction and infrequently postoperative infections. 3D printing (3DP) is a promising technology for the fabrication of personalized medical devices characterised by a more precise and targeted approach to tissue engineering and drug delivery. In this study, blank thermoplastic polyurethane (TPU) and gentamicin sulfate (GNS)-loaded filaments (1 % and 1.5 %wt.) were fabricated with hot melt extrusion (HME) and subsequently processed through 3DP for scaffold manufacturing. Geometrical attributes of the scaffolds, including a specific % infill, were predefined through computer aided design (CAD) and printing parameters were optimised. Physicochemical analysis involving material compatibility and thermal properties of all formulations were examined, determining their thermal and chemical stability during 3DP. Mechanical analysis showed that polymeric matrixes resemble to diaphragm tissue, exhibiting adequate and reproducible elastic performance, while cell studies confirmed TPU's supportive capacity for cellular attachment. Additionally, in vitro dissolution and bacterial studies were carried out for up to a week, denoting GNS's sustained release from the polymeric matrices and efficient bactericidal activity to Gram-positive and Gram-negative bacteria, respectively. Therefore, TPU is a potential biomaterial that can be efficiently used for developing diverse 3D printed diaphragm-like scaffolds possessing antimicrobial activity for CDH.