Head lice infestations significantly impact schoolchildren, with permethrin being the primary treatment. The escalation in the prevalence of the knockdown resistance (kdr) mutation, potentially affecting treatment efficacy, is highly concerning. This study examined head lice infestation prevalence, the efficacy of 1% permethrin lotion, kdr mutation frequency, and the association between kdr genotype and permethrin treatment outcomes in schoolchildren in Nonthaburi province, Thailand. Participants and lice samples were collected from six primary schools using cluster sampling. Clinical outcomes and adverse events were assessed on days 7 and 14 post-treatment. Kdr mutations (T917I) in head lice samples were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Head lice infestation prevalence was 6.1%, with a kdr mutation frequency of 63.2% and a permethrin cure rate of approximately 50%. Multivariate regression analysis revealed the association between kdr genotype and clinical response to permethrin treatment (Odds Ratio (OR) = 13.15, p = 0.005). The presence of resistance genes hinders the cure rate (presence 35.9% versus absence 85.7%). These findings highlight the importance of the kdr genotype in predicting permethrin treatment responses in head lice infestations. Furthermore, in regions with documented reduced permethrin efficacy and a high prevalence of kdr mutations, alternative non-pyrethroid-based pediculicides should be considered. This research could help improve the control of head lice infestations, especially in problematic areas of Thailand.