Nanogels have been recently attracted attentions because they exhibit significantly different behaviors compared with nanoparticles. Among them, chitosan (CS) nanogels have gained considerable attentions from researchers for in vivo applications due to bioactivity, biodegradability, mucoadhesiveness, and biocompatibility of CS. In this review, we have summarized the applications of CS nanogels for efficient drug delivery. Specifically, CS nanogels can be modified by pH-sensitive groups or specific ligands to obtain the corresponding functions. These functional CS nanogels have been used to deliver therapeutic agents, such as anti-cancer drugs, genes, and vaccines. By reviewing the recent research progress on CS nanogels in pharmaceutical applications, it will provide biomaterial researchers potential help for the development of CS nanogel delivery system to meet clinical needs.