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An approach of control design using fuzzy estimators (FEs) is proposed for quantum systems with uncertainties. Two types of quantum control problems are considered: 1) control of a pure-state quantum system in the presence of uncertainties and 2) control design of quantum systems with initial mixed states and uncertainties. For the first type of tasks, a partial feedback control scheme with an FE is presented to design controllers. In this scheme, an FE is trained to estimate the quantum state for feedback control of a quantum system, and controlled projective measurement is used to assist in controlling the system. For the second type of quantum control tasks, a probabilistic fuzzy estimator (PFE) is trained to estimate the quantum state for control design of a quantum system with an initial mixed state, and a corresponding control algorithm is proposed to design a control law that drives the system from the mixed state to a target pure state. Two examples of two-spin-1/2 systems are also presented and analyzed to demonstrate the process of control design and potential applications of the proposed approach.