Due to the side effect of commonly used chemical scolicidals, advantages of micro drug delivery system and growing interest for the phytoceuticals, the present study aimed to find out the scolicidal activity of two volatile terpenes (α-pinene and β-caryophyllene) and their microemulsions on protoscoleces of Echinococcus granulosus. The ordinary and microemulsions of α-pinene and β-caryophyllene and their combination at three different ratios (2:1, 1:1, 1:2) were developed and characterised by dynamic light scattering to confirm micro-dimensions. The scolicidal effect of the developed formulations at the concentrations of 0.5, 1, 2, 5 and 10 μg/mL were measured at 10, 30, and 60-min time points. Mortality rates were recorded by eosin exclusion test. At the 10-min time point, ordinary and micro α-pinene at the concentration of 10 μg/mL killed 94.66% and 100% of the protoscoleces, respectively. At the same time point and concentration, ordinary and micro β-caryophyllene caused 44.33% and 68.66% mortality rates in protoscoleces, respectively. Based on the 50% lethal concentration (LC50) values, there was no significant difference between ordinary and micro-emulsified α-pinene. For the micro β-caryophyllene, a LC50 value of 2.1 µg/mL was obtained which was significantly lower than that of ordinary β-caryophyllene (49.85 µg/mL). No synergistic interaction existed between β-caryophyllene and α-pinene regarding their activity on E. granulosus. Development of microemulsions increased the toxicity of these terpenoids on protoscoleces, especially that of β-caryophyllene, probably due to improved penetration into the parasite. Further studies are needed to assess in vivo efficacy and safety of this specific preparation.