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A partial differential equation (PDE) constrained design optimization problem usually optimizes a characteristic of a dynamical system around an equilibrium point. However, a commonly omitted constraint is the linear stability constraint at the equilibrium point, which undermines the optimized solution’s applicability. To enforce the linear stability constraint in practical gradient-based optimization, the derivatives must be computed accurately, and their computational cost must scale favorably with the number of design variables. In this paper, we propose an algorithm based on the coupled adjoint method and the algorithmic differentiation method that can compute the derivative of such constraint accurately and efficiently. We verify the proposed method using several simple low-dimensional dynamical systems. The relative difference between the adjoint method and the finite differences is between [Formula: see text] to [Formula: see text]. The proposed method is demonstrated through several optimizations, including a nonlinear aeroelastic optimization. The proposed algorithm has the potential to be applied to more complex problems involving large-scale nonlinear PDEs, such as aircraft flutter and buffet suppression.