Objectives Head lice infestation is one of the most important health problems, generally involving children aged 5–13 years. This study aims to estimate the prevalence of head lice infestation and its associated factors among primary school children using systematic review and meta-analysis methods. Methods Different national and international databases were searched for selecting the relevant studies using appropriate keywords, Medical Subject Heading terms, and references. Relevant studies with acceptable quality for meta-analysis were selected having excluded duplicate and irrelevant articles, quality assessment, and application of inclusion/exclusion criteria. With calculating standard errors according to binomial distribution and also considering the Cochrane's Q test as well as I-squared index for heterogeneity, pediculosis prevalence rate was estimated using Stata SE V.11 software. Results Forty studies met the inclusion criteria of this review and entered into the meta-analysis including 200,306 individuals. Using a random effect model, the prevalence (95% confidence interval) of head lice infestation among primary school children was estimated as 1.6% (1.2–2.05), 8.8% (7.6–9.9), and 7.4% (6.6–8.2) for boys, girls, and all the students, respectively. The infestation rate was found to be associated with low educational level of parents, long hair, family size, mother's job (housewife), father's job (worker/unemployed), using a common comb, lack of bathrooms in the house, and a low frequency of bathing. Conclusion This meta-analysis revealed that the prevalence of head lice infestation among Iranian primary school children is relatively high with more prevalence among girls. We also found that economic, social, cultural, behavioral, and hygienic factors are associated with this infestation.