Neonatal fungal endocarditis is a rare but serious infection, which does not have a well-accepted management method. This is the second report of this condition in Saudi Arabia. A preterm, very low birth weight, female neonate presented with fever and shortness of breath. An echocardiogram showed moderate pericardial effusion and two masses in the heart, one in the right ventricle and the other in the inferior portion of the posterior mitral valve of the left ventricle. Blood and pericardial fluid cultures revealed an infection with Candida albicans. The patient received a 60days course of intravenous fluconazole and amphotericin B lipid complex. At the conclusion of treatment, she was discharged in good condition with no echocardiographic evidence of pericardial effusion or fungal vegetations. Thus, a successful outcome to a serious case of fungal endocarditis was achieved through aggressive antifungal therapy with intravenous fluconazole and amphotericin B lipid complex.