Neglected tropical diseases (NTDs) are a diverse group of infections which are difficult to prevent or control, affecting impoverished communities that are unique to tropical or subtropical regions. In spite of the low number of drugs that are currently used for the treatment of these diseases, progress on new drug discovery and development for NTDs is still very limited. Therefore, strategies on the development of new delivery systems for current drugs have been the main focus of formulators to provide improved efficacy and safety. In recent years, particulate delivery systems at micro- and nanosize, including polymeric micro- and nanoparticles, liposomes, solid lipid nanoparticles, metallic nanoparticles, and nanoemulsions, have been widely investigated in the treatment and control of NTDs. Among these polymers used for the preparation of such systems is chitosan, which is a marine biopolymer obtained from the shells of crustaceans. Chitosan has been investigated as a delivery system due to the versatility of its physicochemical properties as well as bioadhesive and penetration-enhancing properties. Furthermore, chitosan can be also used to improve treatment due to its bioactive properties such as antimicrobial, tissue regeneration, etc. In this review, after giving a brief introduction to neglected diseases and particulate systems developed for the treatment and control of NTDs, the chitosan-based systems will be described in more detail and the recent studies on these systems will be reviewed.