This paper describes the development and experimental characterization of a fully-differential, dual-axis wall shear stress sensor system designed to be non-invasive to low-speed aerodynamic flows. The differential capacitive microelectromechanical systems (MEMS) sensor is fabricated using a novel, low-cost approach to creating backside electrical contacts, providing a hydraulically smooth surface without the use of through-silicon vias. Fully-differential, dual-axis sensor electronics provide improved common-mode rejection, reduced environmental sensitivity, and increased shear stress sensitivity, thus increasing the dynamic range of the sensing system. Use of fully-differential charge amplifiers provides improved performance compared to a single-ended voltage amplifier configuration. Initial characterization of the sensor system with differential charge amplifiers yields wall shear stress sensitivities of 4.24 mV/Pa and 6.87 mV/Pa for the two axes, resulting in input-referred minimum detectable signals at 1 kHz of 0.16 mPa and 0.06 mPa, respectively. Dynamic calibration also provides cross-axis rejection ratios of 28.3 dB and 27.4 dB and pressure rejection ratios of 80.7 dB and 77.1 dB.