Giardiasis, caused by Giardia duodenalis, is a common gastrointestinal infection. This study aimed to evaluate the effects of Hedera helix leaf extract (HLE) and HLE-loaded chitosan nanoparticles (HLE-CsNPs) against Giardia duodenalis isolates from individuals with gastrointestinal issues, using an experimental rat model. Stool samples from 147 participants were analyzed for Giardia duodenalis, with positive samples further characterized by nested PCR-RFLP, revealing a 4.8% prevalence, all belonging to assemblage B. Ten groups of male albino rats were used to evaluate the antigiardial activity of various treatments. This included five non-infected groups [one untreated and four treated with HLE, HLE-CsNPs, CsNPs, and metronidazole (MTZ)] and five infected groups [one untreated and four similarly treated]. Treatment efficacy was assessed using parasite counts, intestinal histopathology, CD117 immunohistochemistry, and markers of liver and kidney function. HLE-CsNPs markedly reduced Giardia cysts by 88.8%, approaching the 99.2% reduction achieved by MTZ, while also improving intestinal architecture and reducing inflammation. Importantly, HLE and HLE-CsNPs provided superior protection for the liver and kidneys compared to MTZ. In conclusion, HLE-CsNPs exhibited significant antigiardial activity and organ protection in rats, suggesting a potential alternative treatment for Giardia duodenalis isolated from individuals with gastrointestinal issues.