Introduction Suicide has been recognized as a public health problem with high burden in low and middle income countries. Suicide has long lasting psychological trauma on friends and relatives in addition to loss of economic productivity. Although the need of high quality evidence is acknowledged for designing suicide prevention program, Nepal lacks evidence from reliable and nationally representative data. In this context, this study aimed to estimate the prevalence of suicidal ideation and attempt and identify the factors associated with them. Materials and Methods Total of 6,531 students of grade 7 to 11 from 74 schools representing all three ecological belts and five development regions participated in this cross sectional study. To select the representative sample from study population, we used the two stage cluster sampling method. The respondents filled the self-administed standardized questionnaire. We carried out a Complex survey analysis for adjusting the selection probability of each research participants. Results Nearly 14% had considered suicide while 10.33% had attempted suicide. Factors associated with suicidal ideation were the food insecurity (OR=2.31, CI=1.64-3.27), anxiety (OR=2.53, CI=1.48-4.30), loneliness (OR=2.50, CI=1.41-4.44) and gender (OR=1.38, CI=1.03, 1.88) as risk factors of suicidal ideation and anxiety (OR=2.99, CI=1.18-7.64), loneliness (OR=2.19, CI=1.28-3.74) truancy(OR= 1.99, CI=1.39-2.87), cigarette use(OR=3.06, CI=1.32-7.09) and gender (OR=1.60, CI=1.07-2.39) as risk factors of suicidal attempt. Having 3 or more close friends was found to have protective effect (OR=0.35, CI=0.16-0.74) against suicidal attempt. Conclusion Study reveals the relatively high prevalence of suicidal ideation and suicidal attempt among school-going adolescents in Nepal. Appropriate coping strategies for factors like anxiety, loneliness seem could be useful for preventing both suicidal ideation and attempt.