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Chitosan hydrogel is a smart and highly applicable drug delivery carrier because of its nature, biocompatibility, biodegradability, and ability to encapsulate, carry and release the drug to the desired target flexibly depending on the conditions of the patient. Not only developing delivery systems but natural compounds are also increasingly being studied in supporting the treatment of diseases. However, the physicochemical and pharmacokinetic issues of the phytochemicals are remaining. This review summarizes the remarkable properties of chitosan hydrogel; approaches to loading natural extracts on the hydrogels to overcome the susceptibility of the phytochemicals to degradation; and their applications in biomedical fields. The drug loading efficiency, release profile, in vitro and in vivo results of the chitosan hydrogels carrying natural compounds are discussed to point out the remaining challenges of combining the extracts with chitosan hydrogels and controlling the release of the carried substances.