Aqueous flow cells, including redox flow batteries and regenerative fuel cells, are promising technologies for grid-scale energy storage due to their intrinsic safety, high scalability, and flexibility in decoupling power and energy. Redox active species are critical components of aqueous flow cells as they largely determine the energy density, cell performance, and system cost. Halogens have attracted enormous interest as redox active species for aqueous flow cells due to their low cost, high natural abundance, and desirable electrochemical properties, such as high redox potential and high reversibility. Moreover, halogen species have been widely used as redox mediators and complexing agents to improve the reversibility and solubility of active materials, enabling aqueous flow cells to achieve high energy density and performance. This review provides a comprehensive summary of various types of aqueous flow cells that use halogens as active materials, redox mediators, and complexing agents. The working principles, critical issues, and recent progress are systematically discussed based on the roles and types of halogen species. Finally, existing challenges and future perspectives on halogen-based flow cells are highlighted.