This paper discusses aerodynamic optimization of the high-wing configuration to explore fuselage-wing shapes for the high-wing configurations of near-future aircraft, in which it will be possible to install fuel-efficient, ultrahigh-bypass ratio engines, using computational fluid dynamics simulation and the Kriging surrogate-assisted genetic algorithm. First, optimization of the fuselage upper surface is performed, with exploration of the fairing shape suitable for the high-wing configuration. Second, the aircraft nose shape is also optimized, in addition to the fuselage upper surface, to confirm the possibility of generating higher lift by the fuselage itself. Finally, both the fuselage and the wing shape are optimized to improve the lift-to-drag ratio by alleviating the shock wave over the wing, while sustaining the high lift generation of the high-wing configuration. The final optimized configuration achieves not only a lift-to-drag ratio comparable to the DLR-F6, but also a C_L approximately 1.5 times higher than the DLR-F6. These results indicate the possibility of producing high-wing aircraft that not only employ fuel-efficient ultrahigh-bypass ratio engines, but also have much better aerodynamic performance than low-wing configurations.