Hydatid disease is an economic and public health concern in many countries. Currently, surgery is the main treatment option for hydatid disease. In the surgical treatment of hydatidosis, the use of scolicidal agents is very important due to inactivating live protoscoleces and preventing the recurrence of infection. Therefore, it is necessary to investigate newscolicidal agents and novel medications with higher safety and efficacy. In the previous in vitro studies, the scolicidal effects of the methanolic extracts and aromatic water of Zataria multiflora (Z. multiflora) have been demonstrated. Consequently, in this study, the impact of the nanoemulsion of Z. multiflora essential oil on subcutaneous hydatid cysts was compared with albendazole (ABZ). Fifty laboratory male mice were inoculated with 300 viable protoscoleces subcutaneously on the two sides of the abdomen. Following five months of infection, the remaining infected mice (n=42) were allocated into two treatment and one control (without treatment) groups containing fourteen animals each. Group A received ABZ at the dose of 50 mg/kg for 60 days, group B received the nanoemulsions of Z. multiflora at the dose of 50 mg/kg in drinking water for 60 days, and group C was considered as the control group. All the infected mice were euthanized and necropsied two months post-intervention. Afterwards, the cysts were cautiously collected and their number, size, and weight were compared between the mice of different groups. The mean number of hydatid cysts indicated that the nanoemulsion of Z. multiflora essence had a relative superiority to ABZ. On the other hand, the therapeutic effect of ABZ was higher than the nanoemulsion of Z. multiflora essential oil in terms of the mean weight and mean size of hydatid cysts. However, no significant difference was observed between the groups (P>0.5). Overall, the number, weight, and size of cysts were not significantly different between the groups in this investigation. The lack of satisfactory therapeutic results in this study might be due to the location of hydatid cysts in the subcutaneous space.