BACKGROUND: On March 11, 2011, a magnitude 9.0 earthquake occurred off of Japan’s Pacific coast, which was followed by huge tsunamis that destroyed many coastal cities in the area. Due to the earthquake and subsequent tsunami, malfunctions occurred at the Fukushima Daiichi (Fukushima I) nuclear power plant, resulting in the release of radioactive material in the region. While recent studies have investigated the effects of these events on the mental health of adults in the region, no studies have yet been performed investigating similar effects among children. METHODS AND FINDINGS: This study aims to fill that gap by: 1) assessing the mental health of elementary and middle school children living within the Fukushima prefecture of Japan, and 2) identifying risk and protective factors that are associated with the children’s mental health scores. These factors were quantified using an original demographics survey, the Strengths and Difficulties Questionnaire (SDQ), and the Impact of Event Scale-Revised (IES-R), the latter two of which have been previously validated in a Japanese setting. The surveys were distributed to approximately 3,650 elementary and middle school students during the months of February and March, 2012. The data suggests that those children who had been relocated to the city of Koriyama had significantly higher SDQ scores than those children who were native to Koriyama (p < .05) as well as a control group that lived outside of the Fukushima prefecture (p < .01). Using a multivariate regression, we also found that younger age and parental trauma were significantly correlated with higher SDQ scores (p < .001), while gender, displacement from one's home, and exposure to violence were not. CONCLUSIONS: These results suggest that, among children affected by natural disasters, younger children and those with parents suffering from trauma-related distress are particularly vulnerable to the onset of pediatric mental disturbances.