Literature has repeatedly shown a relationship between hair minerals and metabolic health, although studies in children are currently lacking. This study aims to investigate hair levels of calcium (Ca), copper (Cu), magnesium (Mg), iron (Fe), phosphorus (P), and zinc (Zn) and their association with (1) overweight/obesity and (2) metabolic health in Flemish elementary school girls between 5 and 10 years old. Two hundred eighteen girls participated in this study as part of the baseline ChiBS project. Children were subjected to physical examinations, blood and hair sampling. Hair minerals were quantitatively determined via inductively coupled plasma-mass spectrometry after microwave-assisted acid digestion. Body mass index (BMI) and body fat percentage (BF%) were studied as anthropometric parameters, and a metabolic score (including systolic and diastolic blood pressure, insulin resistance and non-high-density lipoprotein (non-HDL) cholesterol as parameters) was calculated, with higher scores indicating a more unhealthy metabolic profile. Hair Ca, Ca/Mg, and Ca/P positively correlated with the anthropometric parameters. An inverse correlation was observed between Ca, Mg, and Ca/P in hair and the metabolic score. Inverse correlations were also observed for individual metabolic parameters (i.e., diastolic blood pressure, homeostasis model assessment for insulin resistance, non-HDL cholesterol). In particular, girls with a total number of three or more metabolic parameters above the age-specific 75th percentile showed significantly reduced hair Ca, Mg, and Ca/P concentrations. This study showed reduced hair mineral concentrations in young girls with a more unhealthy metabolic profile. Positive associations were observed between some minerals and BMI and BF%.