The purpose of this study is to investigate the factors affecting suicidal thoughts experience of middle school students by gender difference and to investigate the actual relevance of suicidal thoughts experience of middle school students. The subjects were 247 middle school students living in Gyeongsangbuk-do from July to August, 2016. The collected data were analyzed using SPSS 23.0 program. The general characteristics and major variables related to gender were analyzed by number, percentage, and χ2-test. Logistic regression analysis was used to determine the suicidal thoughts experience. The results of the study showed that Male students with suicidal thoughts experienced had experience of sadness or despair that can not do everyday life 5.04(Exp(B)) times higher, the level of stress 2.21(Exp(B)) times higher and subjective health 2.03(Exp(B)) than male students who had not suicidal thoughts experience. In the case of female students, the female students with suicidal thoughts experienced a 3.69(Exp(B)) times higher experience of sadness or despair that can not do everyday life who had not experienced suicide. Therefore, it is necessary for the middle school students to cope with the grief and to cope with the grief and despair. Especially considering the difference between genders is necessary grief and despair easing program or counseling, training for suicide prevention.