In this study, chitosan-silica anion exchange membranes were synthesized using a sol-gel process and nucleophilic substitution reaction. The basic properties of the synthesized ion exchange membranes were assessed, including water uptake, contact angle, ion exchange capacity, vanadium ion permeability, impedance, and conductivity. Furthermore, we used the chitosan-silica membranes as a separator in a single all-vanadium redox flow battery system to investigate their charge-discharge characteristics. We then compared the performance of the chitosan-silica membranes with that of commercially available membranes in terms of impedance as a function of thickness and efficiency. In addition, we studied the relationships between the basic properties and the charge-discharge efficiency of the membranes by varying the concentration of (3-glycidyloxypropyl)tri-methoxysilane (GPTMS). The results demonstrate that the mechanical strength and chemical stability of the synthesized chitosan-silica membranes were enhanced with the increase in GPTMS concentration. The chitosan-silica anion exchange membranes exhibited lower vanadium ion permeability and higher coulombic efficiency, and have a lower cost than their commercial counterparts. The highest measured coulombic efficiency reached 91%.