Encephaloceles and severe cardiac malformations are rare presentations in a newborn. The mechanism of these congenital abnormalities is relatively unknown, but it is hypothesized to be related to genetic, environmental, and maternal risk factors. This case report describes a newborn with an occipital encephalocele associated with severe right ventricular hypoplasia secondary to tricuspid and pulmonary atresia. The patient’s maternal risk factors included obesity, type 2 diabetes mellitus, and everyday tobacco use during pregnancy. Education on preconception planning, management, and counseling is essential as a preventative measure in fetal development and is further emphasized in this case.