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Introduction: Head louse infestation is one of the major public health problems among children worldwide. Several drugs have been developed to treat the infestation. Side effects and drug resistance associated with these drugs limit their applicability. Increasing attention of scientific committees to alternative drugs along with greater effects and lower complications and costs, increase the hope of success for alternative drugs. Materials and Methods: 93 participants (11 men and 82 women) with positively diagnosed with head lice infestation were allocated into two groups using the stratified randomization method. The intervention in one group comprised of Peganum harmala oil applied onto the patient’s hair and scalp and the hair and scalp being washed after 20 minutes once a day. The procedure was performed on the first three days of week one of intervention (phase 1) and reiterated on the subsequent week (phase 2) in a similar manner. The other group applied permethrin shampoo once in the first week of intervention and once in the second week. Results: Permethrin shampoo recovered 7 (29.2%) in day 1, 2 (15.4%) in day 2, 2 (25.0%) in day 3 and 28 (73.7%) in day 11 but Peganum harmala oil recovered 17 (70.8%) in day 1, 11 (84.6%) in day 2, 6 (75.0%) in day 3 and 10 (26.3%) in day 11 (P-value <0.005).   Conclusion: The clearing effects and side effects of Peganum harmala oil and permethrin shampoo are approximately similar in the two-phase application although the oil’s clearing and protective effect is greater than that of the shampoo with its effect occurring earlier than that of the shampoo.