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In recent years, sum-of-squares (SOS) method has attracted increasing interest as a new approach for stability analysis and controller design of non-linear dynamic systems. In this study, the authors present a robust SOS/robust LMI method to design a non-linear controller for longitudinal dynamics of a hypersonic aircraft model with parametric uncertainties. To this end, the control design problem is first formulated as a robust SOS problem. Then, an LMI representation of the robust SOS problem is derived using a proposed algorithm and is solved via a stochastic ellipsoid method. As the simulation results show, the designed robust controller is capable of stabilising the aircraft and following pilot commands under up to 50% variation in aerodynamic coefficients.