Flexible batteries, which maintain their functions potently under various mechanical deformations, attract increasing interest due to potential applications in emerging portable and wearable electronics. Significant efforts have been devoted to material synthesis and structural designs to realize the mechanical flexibility of various batteries. Carbon nanotubes (CNTs) have a unique one-dimensional (1D) nanostructure and are convenient to further assemble into diverse macroscopic structures, such as 1D fibers, 2D films and 3D sponges/aerogels. Due to their outstanding mechanical and electrical properties, CNTs and CNT-based hybrid materials are superior building blocks for different components in flexible batteries. This review summarizes recent progress on the application of CNTs in developing flexible batteries, from closed-system to open-system batteries, with a focus on different structural designs of CNT-based material systems and their roles in various batteries. We also provide perspectives on the challenges and future research directions for realizing practical applications of CNT-based flexible batteries.