Biocompatible self-healing hydrogels are new-generation smart soft materials that hold great promise in biomedical fields. Chitosan-based self-healing hydrogels, mainly prepared via dynamic imine bonds, have attracted broad attention due to their mild preparation conditions, excellent biocompatibility, and self-recovery ability under a physiological environment. In this review, we present a comprehensive overview of the design and fabrication of chitosan-based self-healing hydrogels, and summarize their biomedical applications in tissue regeneration, customized drug delivery, smart biosensors, and three/four dimensional (3D/4D) printing. Finally, we will discuss the challenges and future perspectives for the development of chitosan-based self-healing hydrogels in the biomedical field.