Excessive exposure to Mn can lead to its accumulation in the brain with neurotoxic consequences. In children, elevated Mn has been associated with deficits in certain neuropsychological domains such as cognition, motor function, memory and attention, and in some instances, hyperactivity and behavioral problems. The aim of this study was to evaluate behavioral effects in school-aged children living near a ferro-manganese alloy plant and examine their association with Mn exposure. Occipital hair, toenails and blood samples were collected from 225 children (7–12 years old) enrolled in four elementary schools with different levels of exposure to Mn, based on dust Mn deposition rates. Full data set collection was completed and run from 165 children. Mn in hair (MnH), toenails (MnTn), blood (MnB) and blood lead levels (PbB) were determined by graphite furnace atomic absorption spectrometry. Children's behavior was assessed with the Child Behavior Check List (CBCL) reported by parents. Median levels and range of MnH, MnT and MnB were, respectively, 0.73 μg/g (0.16–8.79), 0.84 μg/g (0.15–9.29) and 8.98 μg/L (1.51–40.43). Median and range of PbB were 1.2 μg/dL (0.2–15.6). MnH and MnB were not associated with any scale of the CBCL behavior scores. We found a positive association between logMnTn and raw total CBCL score (β = 10.17, p = 0.034), adjusting for sex, age, maternal IQ and logPbB. Analyses using Generalized Additive Model showed non-linear associations between MnTn and externalizing behavior (p = 0.035), as well as with the related subscales: aggressive behavior (p = 0.045) and rule-breaking behavior (p = 0.024). Further positive associations were observed between MnTn and thought problems (p = 0.031) and social problems (p = 0.027). These findings corroborate previous studies showing an association between Mn exposures and externalizing behavior. Our results suggest that toenail Mn, as a biomarker of environmental exposure, is associated with disruptive behavior in children living near a ferro-manganese alloy plant.