There is growing concern regarding the effects of toxic element exposure on the development of children. However, little is known about the level of toxic elements exposure in Japanese children. The purpose of this study was to assess the concentrations of multiple elements (aluminum, cadmium, lead, calcium, copper, iron, magnesium, sodium, zinc) in the hair of 118 Japanese young children and to explore the factors associated with their element levels. The element concentration was analyzed by ICP-MS, and children’s food and water intake were assessed by the questionnaire. Results showed that there were no large differences between the level of elements in the hair of Japanese children and those of children in other developed countries. Girls had significantly higher levels of aluminum, copper, and iron (p = 0.000, 0.014, and 0.013, respectively), and boys had a higher level of sodium (p = 0.006). The levels of calcium, iron, magnesium, and sodium in nursery school children were significantly higher than those in kindergarten children (p = 0.024, 0.001, 0.046, and 0.029, respectively). Multiple regression analyses with controlling the confounding variables showed significant negative associations of frequency of yogurt intake with aluminum and lead levels (p = 0.015 and 0.037, respectively). When the children were divided into three groups based on the frequency of yoghurt consumption, viz. L (≤once a week), M (2 or 3 times a week), and H (≥4 to 6 times a week) group, the mean aluminum concentration (µg/g) in the L, M, and H groups was 11.06, 10.13, and 6.85, while the mean lead concentration (µg/g) was 1.76, 1.70, and 0.87, respectively. Our results suggested the validity of hair element concentrations as an exposure measure of essential elements and frequent yogurt intake as a viable measure for protecting children from toxic elements. However, these findings will need to be confirmed in more detailed studies with larger sample sizes in the future.