Thrombus formation within the right ventricle (RV) in the setting of pulmonary atresia with intact ventricular septum (PAIVS) is not a very common occurrence and can be catastrophic. We present the case of a seven-month-old child with PAIVS and RV clot who successfully underwent biventricular repair. We discuss the interesting case and the rationale for management by means of biventricular repair over single ventricle repair when feasible in such a setting.