Congenital heart disease (CHD) is one of the most common types of birth defect with a high morbidity and mortality, particularly in severely malnourished children under five. In this study, we aim to identify the predicting factors for CHD and their outcomes. 694 malnourished children under five years of age admitted between April 2015 and December 2017 constituted the study population. Of them, 64 were cases of CHD, and by comparison 630 were without CHD. CHD was diagnosed clinically and confirmed by echocardiogram. 64% of the cases had a single defect. Cases were more likely to be present with diarrhea, cough, respiratory distress, cyanosis, hypoxemia, hypoglycemia and hypernatremia on admission. The cases also had a high proportion of severe sepsis, bacteremia, heart failure, respiratory failure and death, compared to those without CHD. Cough (95% CI = 1.09–18.92), respiratory distress (95% CI = 1.46–5.39) and hypoxemia (95% CI = 1.59–6.86) were found to be the independent predictors for CHD after regression analysis, and their early identification might be helpful to lessen ramifications, including mortality, in such populations, especially in resource-limited settings.