Natural disasters such as earthquakes can cause substantial damage and trauma, especially to children. The aim of this study was to examine the effects of disaster experience on psychological symptoms, suicide risk, and associated factors in junior high school students 5 years after the Great East Japan Earthquake (GEJE). The hypothesis of this study was that psychological symptoms and suicide risk of junior high school students are associated with disaster experience. A cross-sectional survey consisting of questionnaires and face-to-face interviews with students at two junior high schools in Ishinomaki city, Miyagi Prefecture, Japan, about psychological symptoms, disaster situations, and their current environment 5 years after the GEJE was conducted. In total, data from 264 (117 boys 44.3% and 147 girls 55.7%) students were analyzed. There were no associations between disaster experience and PTSSC-15, DSRS-C, and SCAS scores. Those with evacuation experience and still living in temporary housing had significantly higher scores on the oppositional defiant behavior inventory (ODBI). Of these students, 29 (11.0%) were considered to have suicide risk 5 years after the GEJE. The presence of depressive symptoms was the only factor related to suicide risk; no associations were found with sex, post-traumatic stress disorder (PTSD) symptoms, or other factors reported in previous studies, including disaster experience. Disaster experience was not associated with psychological symptoms (PTSD, depression, anxiety) and suicide risk in junior high school students 5 years after the GEJE. The suicide risk appears to be the same as that in the general population in Japan. However, attention should be paid to externalization problems and depressive symptoms, an important suicide risk factor, even 5 years after the GEJE.