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Background Suicide is the 3 rd leading cause of death among young people. Patients with epilepsy are 2 times more likely to have suicidal ideation and 3 times more likely to plan suicide attempt. In addition to seizures, these young people experience a variety of psychiatric illnesses like depression and anxiety. Social support and coping are known to have an effect on suicidal behavior in adolescents with epilepsy. There’s scanty data on this subject in Uganda. The purpose of this study was to determine the prevalence of suicidal behavior among adolescents with epilepsy at Butabika and Mulago National Referral Hospitals and associated factors. Methods Between 1 st August 2017 and 1 st February 2018, we sampled 223 adolescents from Butabika and Mulago National Referral Hospitals using a cross sectional study design. We used a Demographics Questionnaire, Mini International Neuropsychiatric Interview for Children and Adolescents-DSM-IV-TR version (MINI-KID), Brief COPE, and Multidimensional Scale of Perceived Social Support (MSPSS) to collect data. Data Entry was done using Epi Data and analyzed with Stata version 14. The dependent variable was suicidal behavior and independent variables were socio-demographic characteristics of adolescents and caregivers, epilepsy related factors, psychiatric co morbidity, coping strategies and perceived social support. Bi-variate and Multi-variate analyses were done to describe the associations between the dependent and independent variables. Results Of the 223 adolescents we recruited, (123)55.2% were male, 52.9% were aged 14-17 years. The prevalence of suicidal behavior was 30.5%. Major depression was most strongly associated with suicidal behavior (aOR=9.3, CI=4.3-20.1, p<0.001). Adolescents having post primary education were more likely to have suicidal behavior (aOR=2.2, CI=1.0-4.9, p=0.046). Venting as a coping strategy was found to increase the likelihood of having suicidal behavior (aOR=2.7, CI=1.2-6.2, p=0.017) whereas perceived family social support (aOR=0.4, CI=0.2-0.8, p=0.017) and the use of the active coping strategy (aOR=0.4, CI=0.2-0.9, p=0.033) were protective against suicidal behavior. Conclusions Prevalence of suicidal behavior in adolescents with epilepsy is high. Major depression is associated with suicidal behavior while perceived family social support is protective against suicidal behavior.