We characterize the electroosmotic flow in a microchannel with field effect flow control. High resolution measurements of the flow velocity, performed by micro particle image velocimetry, evidence the flow reversal induced by a local modification of the surface charge due to the presence of the gate. The shape of the microchannel cross-section is accurately extracted from these measurements. Experimental velocity profiles show a quantitative agreement with numerical results accounting for this exact shape. Analytical predictions assuming a rectangular cross-section are found to give a reasonable estimate of the velocity far enough from the walls.