A 65 year-old female was admitted with acute pulmonary embolism and hypotension. Intravenous streptokinase was administered but severe hypotension persisted. Pulmonary angiography was performed and partial recanalisation of the culprit branch was noted. Echocardiography showed severe right ventricular (RV) dysfunction and free wall akinesia. Due to exaggerated RV dysfunction and severe haemodynamic compromise a coronary angiography was done and showed abnormal origin of right coronary artery (RCA) from left circumflex artery (LCx) with rudimentary RV branches and absent conus artery and right atrial (RA) branch. Inotropic agents were necessary to stabilize the patient's haemodynamic condition for the next four days. We concluded that this coronary anomaly was an important contributory factor in our patient's prolonged unstable condition. This emphasizes the critical role of normal RCA flow under acute haemodynamic stress. Evaluation of the condition of RV perfusion and RCA patency might be justified in any prolonged and disproportionate RV dysfunction following acute pulmonary embolism.