Background and Objective: Head louse (Pediculus humanus capitis) is one of the most important parasites in humans and applying permethrin is the standard method for its control. Continuous application of this chemical increases the probability of permethrin resistance and gradually the addition of alternative substances is necessary. The aim of this study was evaluation of the efficacy of eucalyptus and cinnamon essential oils in head lice treatment compared to permethrin. Materials and Methods: The essential oils of Eucalyptus globules and Cinnamomum zeylanicum were extracted using a hydrodistilation method and their components were identified via gas chromatography. In the single-blind clinical trial, 95 infested cases residing in Zanjan were categorized into groups of 34, 31 and 30, receiving eucalyptus, cinnamon and permethrin treatment respectively. The lice infestation and hatching rate of nits were investigated before and after the intervention. Results: The major components of eucalyptus and cinnamon were 1,8-cineole, alpha-pinene, cinnamaldehyde, and 2-propenal, 3-phenyl respectively. The hatching rate of nits was equal in study groups before the intervention. Eucalyptus shampoo showed a higher therapeutic effect than the other substances (p < 0.06). Mortality rates of nits before and after the treatment with eucalyptus and permethrin showed a significant difference (p= 0.009), whereas this difference was non-significant with cinnamon (p= 0.08). The efficacy of cinnamon and permethrin shampoos was equal (p= 0.139). The comparison of nit mortality rates showed a significant difference between the eucalyptus-cinnamon groups (p= 0.06), while differences between the eucalyptus-permethrin groups and the cinnamon-permethrin groups were non-significant (p> 0.28). Conclusion: Eucalyptus essential oil had a greater therapeutic effect on head lice. This compound is recommended as an alternative to permethrin or for use in combination with permethrin in the head lice control program. © 2017, Zanjan University of Medical Sciences and Health Services. All Rights Reserved.