This paper presents the optimization of multi-element aerofoil for the LAR-3 Puffin -- STOL light transport aircraft concept proposal. Based on the geometry and aerodynamic characteristics of the well-known and proven in flight three-segment NACA 63A416 aerofoil, the authors explore the possibility of enhancing its high-lift performance by the movement of slot and flap position in extended (deployed) aerodynamic configuration. In order to determine the optimum positions of aerofoil segments (elements), a multi-step optimization approach was developed. It combines computational fluid dynamics simulations that were used for design space screening and preliminary optimization together with low-turbulence wind tunnel tests which yielded certain results. To decrease the numerical cost of the computer simulation campaign, Design of experiment methods (optimal space-filling design among others) were employed instead of exhausting full factorial (parametric) design. Response surface models of major aerodynamic coefficients (lift, drag, pitching moment) at predicted maximum lift coefficient ( C L max) point allowed to narrow down search space and identify several candidates for optimal configuration to be checked experimentally. Wind tunnel tests campaign confirmed the major trends observed in computational fluid dynamics derived response surface contour plots. For the optimum aerodynamic configuration, chosen experimental C L max is over 3.9, which is a 10% increase over the baseline (initial slat and flap positions) case. In parallel, the maximum lift-to-drag ratio gain at that point was almost 19%. The research outlined in this paper was conducted on behalf of the aircraft production company and its results will be applied in a newly designed transport aircraft.