The AlGaN/GaN materials with a wide band gap, high electron mobility, and high breakdown voltage are suitable for manufacturing high-power and high-frequency electronic devices. In this study, metal Schottky contact electrodes of different dimensions are prepared on AlGaN/GaN wafers to fabricate metal–semiconductor–metal (MSM) varactors. Voltage-dependent capacitance and breakdown voltages of the varactors are measured and studied. The corresponding breakdown mechanisms of varactors with different electrode gaps are proposed. Furthermore, an anti-surge application using GaN-based MSM varactors in a signal transmission module is demonstrated, and its surge suppression capability is shown. We believe that our study will be beneficial in developing surge protection circuits for RF applications.