In this work, we propose a method that considers the dynamic elastic stiffness of mechanical components in a quasi-static condition, and we investigate this parameter’s effect on gear mesh misalignment. Unlike conventional approaches, which consider static stiffness only, the proposed method allows compensation of the dynamic response of the gearbox components under the quasi-static assumption, enabling more precise and practical gear design. A two-stage parallel gearbox is presented, designed, and numerically analyzed. The results demonstrate that the dynamic stiffness has a significant effect on gear misalignment and should, therefore, be carefully considered in the gear design process.