Flow counterbalanced capillary electrophoresis (FCCE) offers a powerful approach to realizing difficult charge based separations in compact microchip devices with application of relatively small electrical voltages. The need for dynamically controlling the pressure-gradient in the FCCE column however presents a significant challenge in implementing this technique on the microchip platform. In this article, we report the use of a simple on-chip pumping unit that allows precise introduction of a periodic pressure-driven backflow into a microfluidic separation channel enabling an FCCE analysis. The backflow in our device was produced by fabricating a shallow segment (0.5 μm deep) downstream of the analysis column (5 μm deep) and applying an electric field across it. A mismatch in the electroosmotic transport rate at the interface of this segment was shown to yield a pressure-gradient that could reverse the flow of the analyte bands without inverting the direction of the electric field. Although such a pressure-gradient also led to additional band broadening in the system, overall, the separation resolution of our device was observed to improve with an increasing number of back-and-forth sample passes through the analysis channel. For our current design, the corresponding improvement in the effective separation length was as much as 52% of the actual distance travelled by the chosen FITC-labeled amino acid samples. The reported device is well suited for further miniaturization of the FCCE method to the nanofluidic length scale which likely would improve its performance, and is easily integrable to other analytical procedures on the microchip platform for lab-on-a-chip applications.