Human biomonitoring is a reliable method for evaluating human exposure to specific contaminants. Although blood is an ideal matrix for monitoring purposes, it is regarded as an invasive matrix. Therefore, current developments in the field of human biomonitoring are based on introducing new methods that use non-invasive matrices, such as hair. In this study, we examined the efficiencies of several extraction methods for the analysis of hexabromocyclododecane (HBCD) and tetrabromobisphenol-A (TBBPA) in human hair. The selected pretreatment method was validated through a general QA/QC process that included spiking experiments, and then, the method was used for the determination of HBCD and TBBPA concentrations in scalp hair samples collected from individuals in Korea (n = 24) and Iran (n = 15). The HBCD and TBBPA concentrations in the collected hair samples ranged from ND to 3.24 ng g−1 and ND to 16.04 ng g−1, respectively. Significantly higher concentrations of TBBPA were found in hair samples from Korea than those in hair samples from Iran (p < 0.05), which is expected to be the result of the large market and higher exposure of TBBPA in Korea. HBCD was not detected in hair samples from Iran. According to our knowledge this is the first study demonstrating the presence of TBBPA in human hair with nonspecific exposure. Lastly, we investigated the important factors that influence the interpretation of the contributions of endogenous and exogenous contaminations in hair. Based on the information, the HBCD and TBBPA in the collected hair samples were most likely from endogenous exposure. Therefore, our study showed that hair is potentially a suitable indicator for the monitoring of internal exposure to HBCD and TBBPA in different populations.