A field-effect transistor is developed to control flow in microfluidic chips by modifying the surface charge condition. In this investigation, zeta potential at a particular location is altered locally by applying a gate voltage, while zeta potential at other locations is maintained at its original value. This non-uniform zeta potential results in a secondary electroosmotic flow in the lateral direction, which is used for flow control in microgeometries. Here, microchannel structures and field-effect transistors are formed on polydimethylsiloxane (PDMS) using soft lithography techniques, and a micro particle image velocimetry technique is used to obtain high resolution velocity distribution in the controlled region. The flow control is observed at relatively low gate voltage (less than 50 V), and this local flow control is primarily due to current leakage through the interface between PDMS and glass layers. 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. This leakage-current based field-effect is then applied to a T-channel junction to control flow in the branch channel. Experiments show that the amount of discharge in the branch channel can be controlled by modulating gate voltage.