This paper presents a novel method for multi-objective optimisation under uncertainty developed to study a range of mission trade-offs, and the impact of uncertainties on the evaluation of launch system mission designs. A memetic multi-objective optimisation algorithm, MODHOC, which combines the Direct Finite Elements transcription method with Multi Agent Collaborative Search, is extended to account for model uncertainties. An Unscented Transformation is used to capture the first two statistical moments of the quantities of interest. A quantification model of the uncertainty was developed for the atmospheric model parameters. An optimisation under uncertainty was run for the design of descent trajectories for the Orbital-500R, a commercial semi-reusable, two-stage launch system under development by Orbital Access Lt