Abstract Background Arteriovenous malformation of the vein of Galen with partial anomalous pulmonary venous return can lead to a critically challenging condition associated with a high morbidity and mortality. Case report We report a case of a full term infant born with a vein of Gallen arteriovenous malformation complicated by partial anomalous pulmonary venous return and congestive heart failure where B-type natriuretic peptide was used as a vital tool in clinical assessment and treatment management. Conclusions Rapid diagnosis and treatment in infants with complex conditions such as this are imperative to expedite appropriate treatments, preventing long term negative outcome.