Background: Undernutrition and cardiac disease are interconnected in a vicious cycle. Children with cardiac disease suffer with different degree of undernutrition resulting in significant morbidity and mortality in developing countries. This study aimed to assess magnitude of undernutrition and associated factors among children with cardiac disease in University of Gondar hospital, northwest Ethiopia. Method: Hospital based quantitative cross-sectional study conducted among 269 children with cardiac disease visiting University of Gondar specialized hospital, northwest Ethiopia. Data was collected by using a pretested self-administered structured questionnaire and medical records of the patients. All participants who fulfill the inclusion criteria were included. The data analysed by using binary logistic regression model. Variables with p-value ≤ 0.2 in bivariate analysis were fitted to the final multivariable analysis and those variables with p-value ≤ 0.05 were considered as having statistically significant association to the outcome variable. AOR and 95% confidence interval was calculated to assess the strength of association between the variables. Result: Of the 269 study participants, 177(65.7%) of them were having undernutrition. 54.5% were underweight, 39.7% were stunted, and 53.9 % were wasted. The result showed that having pulmonary hypertension[AOR =3.82, (95%CI 1.80, 8.10)], NYHA/modified Ross class III and IV heart failure[AOR=4.64(1.69, 12.72)] and cardiac chamber enlargement [ AOR=2.91(1.45, 5.66)] were significantly associated with undernutrition. Conclusion: There is high burden of undernutrition among children with cardiac diseases in the study area. Nutritional management and dietary counseling besides early detection and treatment of the underlying heart disease improves the nutritional status of children with cardiac diseases.