Children’s development and health may be affected by toxic heavy metal exposure or suboptimal essential element intake. This study aimed to provide updated information regarding the concentrations of 41 elements in children’s hair (aged under 18) living in a rural area of the Benishangul-Gumuz region, Ethiopia. The highest average levels (as a geometric mean) for toxic heavy metals were obtained for Al (1 mg kg−1), Pb (3.1 mg kg−1), and Ni (1.2 mg kg−1), while the lowest concentrations among the essential elements were found for Co (0.32 mg kg−1), Mo (0.07 mg kg−1), Se (0.19 mg kg−1), and V (0.8 mg kg−1). Hair analysis was combined with a survey to evaluate relationships and variations among subgroups and potential metal exposure predictors. Females showed significantly higher concentrations for most hair elements, excluding Zn, than males, and the 6–11 years age group reported the highest levels for Be, Ce, Co, Fe, La, Li, Mo, and Na. The main predictors of exposure to toxic elements were fish consumption for Hg and drinking water for Ba, Be, Cs, Li, Ni, Tl, and U. The data from this study can be used to develop prevention strategies for children’s health and protection in developing countries.