In this paper we propose a sliding mode controller for a MIMO model of flow separation in boundary layers. The model consists in a bilinear system with constant delays in both the state and the input. The main motivation to consider such a class of systems is that, it has shown to be suitable for input-output modelling and control design of some turbulent flow control systems. Stability and robustness properties of the control scheme are studied by means of Volterra equations theory, which provides easily verifiable stability conditions.