Chitosan, as a unique positively charged polysaccharide, has been one of the most popular biopolymers for development of drug delivery systems for various applications, due to its promising properties, including high biocompatibility, excellent biodegradability, low toxicity, as well as abundant availability and low production cost. Since last decade, increasing attention has been attracted by delivery systems fabricated from natural biopolymer-based polyelectrolyte complexes (PEC), formed by electrostatic interactions between two oppositely charged biopolymers. In order to tailor specific applications of chitosan-based PEC drug delivery systems, various forms have been developed in recent years, including nanoparticles, microparticles, beads, tablets, gels, as well as films and membranes. The present review focuses on the recent advances in drug delivery applications of chitosan-based PEC with other natural polysaccharides, including alginate, hyaluronic acid, pectin, carrageenan, xanthan gum, gellan gum, gum arabic, and carboxymethyl cellulose, etc. The fabrication techniques, characterizations, as well as in vitro and in vivo evaluations of each PEC delivery system are discussed in detail.