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Abstract Vanadium dioxide (VO2) undergoes a metal-insulator transition (MIT) at approximately 68 °C, with associated sharp changes in its physical (e.g., optical, electrical, and mechanical) properties. This behavior makes VO2 films of interest in many potential applications, including memory devices, switches, sensors, and optical modulators. For ON/OFF like digital applications, an abrupt switching behavior is ideal. However, to continuously change VO2 metal/insulator phase ratio for analog-like operation, the intrinsic hysteresis characteristic of VO2 MIT renders the phase control becoming a formidable challenge. This paper considers the problem of controlling and tracking desired optical transmittance via continuous phase ratio change. The problem becomes worse while considering the differences of individual thin-film samples and the hysteresis associated with the phase change within a narrow temperature range. This paper reports a robust feedback controller using an optical transmittance measurement and based on an uncertainty and disturbance estimator (UDE) architecture. The proposed controller is capable of mitigating the adverse effect of hysteresis, while also compensating for various uncertainties. The effectiveness of the proposed methodology is demonstrated with experimental validation.