This paper presents a multi-disciplinary analysis methodology for a box-wing aircraft configuration optimised for a given mission scenario. This conceptual design methodology and associated toolchain combines well-established vortex lattice analysis and a newly developed structural analysis tool called WingMASS, allowing the design space to be explored from a combined aerodynamics and structural design perspective. For a given mission scenario, the method optimises a box-wing configuration and compares it with an equivalent conventional configuration. This study shows that, for a given mission, a box-wing configuration can lead to a fuel burn reduction of up to 5% by optimising aspect ratio, horizontal and vertical wing separation.