We propose a method to design reduced-order output-feedback controllers for fluid flows with the use of data produced by full-order controllers. First, the full-order controller is obtained by combining an ensemble Kalman filter (EnKF) and a model predictive controller (MPC) that are designed based on the Navier–Stokes equations. The full-order controller has high computational complexity and, therefore, is not suitable for real-time implementation. Hence, we use the full-order controller in offline numerical simulations to generate data for data-driven design of the reduced-order controller with low computational complexity. We find a reduced-order subspace of a closed-loop system under the full-order control from the data. This subspace underlies the reduced-order output-feedback controller. The reduced-order state-feedback law is obtained by approximating the full-order MPC with the use of its input/output data. The reduced-order observer is designed for a reduced-order model that is derived by using the Gaussian process regression (GPR). The GPR enables us to design the reduced-order observer which can evaluate uncertainty due to state-dependent residuals of the reduced-order model. We demonstrate the proposed method for a control problem of a flow around a cylinder at the Reynolds number 100. Numerical simulations reveal that the reduced-order controller performs as almost well as the full-order controller for a set of initial states. In addition, robustness of the reduced-order controller to a temporal disturbance that is not considered in the control design is confirmed in the simulations.