Abstract Background Replacement of the right ventricular outflow tract (RVOT) is necessary in many critical congenital heart disease subtypes, often when the child is less than one year old. Poor availability of small-diameter cardiac homografts necessitates the use of xenografts in paediatric surgical reconstruction. Currently used xenografts are limited by immunoincompatibility and lack of growth, requiring repeat surgery to replace the defective graft. One approach to tackle acute immune rejection of animal tissue is aldehyde fixation of grafts prior to xenotransplantation. Though masking antigenicity, fixation is associated with multiple issues, including toxicity of fixative remnants and calcification. Decellularisation of biological grafts to remove foreign material is a promising alternative to reduce immunogenicity and dampen the risk of rejection. To combat lack of growth, in vitro cellularisation with stem cells is a promising solution. Purpose Current RVOT substitutes have not proven to be a lifelong solution for paediatric cardiac repair. This research has optimised a novel decellularisation technique for porcine RVOTs to produce a durable and cell-free scaffold with translational capability. Current work is looking to seed mesenchymal stem cells (MSCs) onto the acellular RVOT in vitro to enhance immune tolerance and endow the graft with growth capacity upon implant. Methods First, this decellularisation technique produces acellular RVOT scaffolds by simultaneously utilising three methods: enzymatic, chemical, and mechanical decellularisation. Novel to this method, the latter is realised using a 3D printed flow chamber to utilise the shear forces of continuous fluid flow for cell removal from the external and internal RVOTs structure. Coating the acellular graft with poly-lysine has then enabled recellularisation with MSCs isolated from the umbilical cord. Results Nuclei quantification demonstrates decellularisation of all structures of the RVOT, and elimination of residual nucleic acids is evidenced. Immunohistochemical analysis confirms the xenoantigen Galα1-3Galβ1-4GlcNAc-R is absent from the decellularised tissue. In parallel with removal of typical immunogens associated with the rejection response, the elastin and collagen fibres of the extracellular matrix are maintained, supported by histology and electron microscopy. Importantly, the tensile properties of the decellularised grafts are preserved. Finally, MSCs adhered onto the external pulmonary artery surface in vitro, achieving a uniform monolayer of cells. Conclusion RVOTs have been successfully decellularised and proven to possess seeding potential. Future work aims to characterise the seeded MSCs to assess parameters including proliferative capacity and expression of typical MSC markers. Overall, this work has the potential to produce a non-immunogenic graft possessing growth potential as a surgical alternative for paediatric RVOT replacement.