Cystic echinococcosis is a major parasitic and zoonotic disease and surgery is the most common treatment of this disease which carries the risk of intraoperative leakage and recurrence. Using scolicidal agent to inactivate cyst contents reduces the risk of recurrence. Considering side effects of available scolicidals and growing interests on natural pharmaceuticals, the present study aimed to evaluate toxicity of cinnamaldehyde (CA), the main component of cinnamon essential oil, and a developed nanoemulsion of cinnamaldehyde (nano-CA) on protoscoleces of hydatid cyst. Nanoemulsion was prepared by the low energy system and characterized by dynamic light scattering to confirm dimensions. For evaluation of scolicidal effects, serial dilutions of CA and nano-CA were mixed with protoscolices suspension and mortality were recorded at 10, 30, and 60 minutes by eosin exclusion test. Albendazole was used as the positive control. The mean diameter of nano-CA was characterized as equal to 88.5 nm, and poly dispersity index was 0.09. After 30 min of treatment, nano-CA, at 50 μg/ml, killed 99.33% of protoscoleces. At the same time point and concentration, CA only caused mortality rate of 26.18%. 30 min-LC50 value of 369.39 μg/ml was obtained for CA, while after 30 min of exposure, nano-CA showed promising rapid activity with LC50 value of 3.22 μg/ml. Nano formulation significantly increased scolicidal activity of CA probably by increasing penetration and tegumental disorganization of protoscoleces. Further in vivo safety studies are needed to introduce nano-CA as a clinically applicable scolicidal agent.