BACKGROUND: Atrial septostomy has been successfully used in patients with pulmonary hypertension and in those supported with veno-arterial extracorporeal membrane oxygenation (VA-ECMO) complicated by pulmonary congestion. CASE DESCRIPTION: We report a patient on VA-ECMO for decompensated pulmonary hypertension who subsequently developed stress-induced cardiomyopathy and pulmonary congestion. An atrial septostomy was performed, which led to worsening respiratory status due to the creation of a right-to-left shunt, and hemodynamic deterioration resulting from increased left ventricular preload. CONCLUSION: The implications of atrial septostomy should be carefully considered prior to decompression, as there may be situations, especially if right-sided pressures are less than left-sided pressures, where patients may still benefit.