After the Great East Japan Earthquake and the subsequent nuclear reactor accident, the outdoor activities of children greatly decreased. We investigated adverse effects on the exercise habits and mental health of children after the disaster. The target subjects were children aged 6 to 15 years living inside the government-designated evacuation zone as of March 11, 2011 (n = 29 585). The subjects’ parents/guardians completed the Strengths and Difficulties Questionnaire (SDQ) and exercise habit data were obtained from the 2011 Fukushima Health Management Survey. A total of 18 745 valid responses were returned. We excluded questionnaires with incomplete answers leaving 10 824 responses for the final analysis. SDQ scores >=16 indicated high risk of mental health. Children in the evacuation zone who did not get regular exercise had a higher risk of mental problems as evaluated by SDQ (multivariate-adjusted prevalence ratio [PR] = 1.49; 95% CI 1.38-1.62). When stratified by sex, age, place of residence, treatment for illnesses and experienced the nuclear reactor accident the associations were essentially the same. Regular exercise is important for maintaining children’s mental health after a disaster. This is the first large-scale report to examine the impact of outdoor exercise limitations among children in a nuclear accident.