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When submerged under a liquid, the microstructure of a SuperHydrophobic Surface (SHS) traps a lubricating layer of gas pockets, which has been seen to reduce the skin friction of the overlying liquid flow in both laminar and turbulent regimes. More recently, spatially homogeneous SHS have also been shown to delay laminar–turbulent transition in channel flows, where transition is triggered by modal mechanisms. In this study, we investigate, by means of topology optimization, whether a spatially inhomogeneous SHS can be designed to further delay transition in channel flows. Unsteady direct numerical simulations are conducted using the spectral element method in a 3D periodic wall-bounded channel. The effect of the SHS is modelled using a partial slip length on the walls, forming a 2D periodic optimization domain. Following a density-based approach, the optimization procedure uses the adjoint-variable method to compute gradients and a checkpointing strategy to reduce storage requirements. This methodology is adapted to optimizing over an ensemble of initial perturbations. This study presents the first application of topology optimization to laminar–turbulent transition. We show that this method can design surfaces that delay transition significantly compared to a homogeneous counterpart, by inhibiting the growth of secondary instability modes. By optimizing over an ensemble of streamwise phase-shifted perturbations, designs have been found with comparable mean transition time and lower variance.