This article presents a detailed aerodynamic investigation on a transport aircraft with a box-wing lifting system. The aerodynamic development of this configuration is presented through the description of the collaborative and multi-fidelity design approach that took place within PARSIFAL, an European project aiming to develop the box-wing configuration for a civil transonic aircraft. The article starts from an accurate description of the collaborative methodological framework employed and offers an overview of the development of the box-wing aerodynamics together with the highlight on its most significant characteristics and aerodynamic features identified. The design development is detailed step by step, with specific focus on the challenges faced, starting from the conceptual investigations up to the most advanced evaluations. Significant focus is given to the assessment of the aerodynamic performance in transonic flight for the box-wing lifting system, and to the design solutions provided to overcome issues related to this flight regime, such as drag rise and flow separation. In addition, the high-fidelity shape optimisation techniques employed in the advanced stage of the design process are detailed; these allow to define a final configuration with improved aerodynamic performance.