Active gust load alleviation techniques exhibit a high potential in significantly reducing the transient gust loads on aircraft. In this work the aerodynamic potential of trailing-edge flaps and leading-edge flaps is numerically studied with the purpose to significantly reduce the structural gust loads. The utilized spanwise-segmented flaps represent slight modifications of existing devices for high-lift and maneuvering. The investigations based on unsteady Reynolds-averaged Navier–Stokes computations are conducted by employing a generic wing–fuselage aircraft configuration at transonic flow conditions. Idealized discrete “”-type vertical gusts that are relevant for the certification process are used as representative atmospheric disturbances. The focus of this paper is to introduce a practicable prediction method for required trailing- and leading-edge flap deflections for a significant mitigation of gust-induced wing loads. The three-dimensional flap deflections are determined by parametric two-dimensional simulations at representative wing sections. Different extensions of the estimation approach are investigated to assess the influence of the wing planform, the finite wing span, the aerodynamic phase lags, and the flap scheduling. It is shown that the trailing- and leading-edge flaps are promising in terms of alleviation of gust-induced wing bending and wing torsional moments, respectively. However, at high leading-edge flap deflections that are necessary for a full compensation of the wing torsional moment large-scale flow separation is identified. The introduced gust load alleviation approach indicates a good transferability between two-dimensional airfoil and three-dimensional wing aerodynamics for unsteady flap deflections.