A reduced-order linear feedback controller, which is used to control the linear disturbance in two-dimensional plane Poiseuille flow, is applied to a boundary layer flow for stability control. Using model reduction and linear-quadratic-Gaussian/loop-transfer-recovery control synthesis, a distributed controller is designed from the linearized two-dimensional Navier-Stokes equations. This reduced-order controller, requiring only the wall-shear information, is shown to effectively suppress the linear disturbance in boundary layer flow under the uncertainty of Reynolds number. The controller also suppresses the nonlinear disturbance in the boundary layer flow, which would lead to unstable flow regime without control. The flow is relaminarized in the long run. Other effects of the controller on the flow are also discussed.