Abstract Background Mental health is a neglected area of health research and practice in most of sub-Saharan African countries where the largest burden of morbidity is from infectious diseases. This even occurs despite the fact that some mental health problems may arise from infectious diseases. Methods We conducted secondary analysis of the Uganda Global School-Based Health Survey-2003 to obtain the prevalence of, and assess factors that may be associated with suicidal ideation among school-going adolescents in rural Uganda. Assessment of association was conducted through both bi-variate and multivariate logistic regression analysis. Results Altogether 21.6% of the study participants, 21.3% males and 23.5% females had seriously considered committing suicide within the past 12 months. Loneliness, worry were positively associated with suicide ideation after adjusting for age, gender, smoking, drinking, and experience of having been bullied (OR = 1.59; 95% CI [1.12, 2.26] and OR = 1.19; 95% CI [1.12, 2.25]) respectively. Males were less likely to seriously consider committing suicide than females (OR = 0.70; 95% CI [0.50, 0.98]). Conclusion Adolescent suicidal ideation is a major public health issue in rural Uganda. Measures aimed to prevent adolescent suicides in Uganda should incorporate our understanding of factors that are associated with suicide in rural Uganda such the gender disparity and the association observed with substance use.