A field-effect transistor is developed on PDMS microchannel to control flow in microfluidic chips by modifying the surface charge condition. By applying a gate voltage to one side of the microchannel wall, zeta potential at that side is altered, while the zeta potential at the other side is maintained at the original value. This non-uniform zeta potential results in a secondary electroosmotic flow in lateral direction, which is used for flow control in microchannel geometries. The flow control is observed both quantitatively and qualitatively at relatively low voltage (less than 50 [V]), and this local flow control is primarily due to the leakage current through the interface between PDMS and glass layers. To verify the experimental results, a leakage capacitance model is introduced to estimate the modified zeta potential for the straight channel case, and excellent agreement is obtained between the predicted and experimental zeta potential results.