Since there is no potential, effective vaccine available, treatment is the only controlling option against hydatid cyst or cystic echinococcosis (CE). This study was designed to systematically review the in vitro, in vivo, and ex vivo effects of nanoparticles against hydatid cyst. The study was carried out based on the 06- PRISMA guideline and registered in the CAMARADES-NC3Rs Preclinical Systematic Review and Meta-analysis Facility (SyRF) database. The search was performed in five English databases, including Scopus, PubMed, Web of Science, EMBASE, and Google Scholar without time limitation for publications around the world about the protoscolicdal effects of all the organic and inorganic nanoparticles without date limitation in order to identify all the published articles (in vitro, in vivo, and ex vivo). The searched words and terms were: “nanoparticles”, “hydatid cyst”, “protoscoleces”, “cystic echinococcosis”, “metal nanoparticles”, “organic nanoparticles”, “inorganic nanoparticles, “in vitro”, ex vivo”, “in vivo”. Out of 925 papers, 29 papers including 15 in vitro (51.7%), 6 in vivo (20.7%), ex vivo 2 (6.9%), and 6 in vitro/in vivo (20.7%) up to 2020 met the inclusion criteria for discussion in this systematic review. The results demonstrated the most widely used nanoparticles in the studies were metal nanoparticles such as selenium, silver, gold, zinc, copper, iron nanoparticles (n = 8, 28.6%), and metal oxide nanoparticles such as zinc oxide, titanium dioxide, cerium oxide, zirconium dioxide, and silicon dioxide (n = 8, 28.6%), followed by polymeric nanoparticles such as chitosan and chitosan-based nanoparticles (n = 7, 25.0%). The results of this review showed the high efficacy of a wide range of organic and inorganic NPs against CE, indicating that nanoparticles could be considered as an alternative and complementary resource for CE treatment. The results demonstrated that the most widely used nanoparticles for hydatid cyst treatment were metal nanoparticles and metal oxide nanoparticles, followed by polymeric nanoparticles. We found that the most compatible drugs with nanoparticles were albendazole, followed by praziquantel and flubendazole, indicating a deeper understanding about the synergistic effects of nanoparticles and the present anti-parasitic drugs for treating hydatid cysts. The important point about using these nanoparticles is their toxicity; therefore, cytotoxicity as well as acute and chronic toxicities of these nanoparticles should be considered in particular. As a limitation, in the present study, although most of the studies have been performed in vitro, more studies are needed to confirm the effect of these nanoparticles as well as their exact mechanisms in the hydatid cyst treatment, especially in animal models and clinical settings.