The Super Proton Synchrotron (SPS) injection system plays a fundamental role to preserve the quality of injected high-brightness beams for the LHC physics program and to maintain the maximum storable intensity. The present set-up is the result of years of upgrades and patches of a system that was not conceived for such intensities and beam qualities. In this study, we propose the design of a completely new injection system based on multi-level numerical optimisation of the different constraints, including realistic hardware assumptions. We present the different algorithms and procedures applied in the optimisation process, and we also outline how this generic optimisation framework can be adapted to other situations for optimal accelerator system design.