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In this study, a stable observer‐based feedback controller has been designed for treatment of hepatitis C infectious disease under interferon (IFN) therapy. In order to consider the memory behavior and uncertain nature of this biological system, an unknown dynamics fractional‐order (FO) model has been utilized for describing the interactions between the healthy cells, infected cells, and hepatitis C virus (HCV). To cope with unknown dynamics, the fuzzy logic system (FLS) has been utilized. Limitation of the drug efficacy due to its negative side effects has been taken into account as an input saturation. In order to estimate the unknown states which are required for treatment, a full‐order fuzzy observer has been designed. Stability of the closed‐loop system in the presence of observer dynamics, input limitation, and unknown system dynamics has been established via the Lyapunov stability theorem. Finally, the effectiveness of the proposed controller has been demonstrated via a simulation study. Simulation results indicate that under the proposed treatment strategy, all system states remain bounded, and the infected cells concentration decreases to the cure boundary.