Stroke and intracranial hemorrhage (ICH) are serious complications that are difficult to manage during surgery for active infectious endocarditis (AIE). Relevant society guidelines still recommend delaying the cardiac surgery for AIE with ICH for 4 weeks. Some early studies indicated that the mortality rate decreases when cardiac surgery for ICH is delayed. In contrast, some reported that surgical intervention should not be delayed if an early operation is demanded, even in patients with ICH. The current literature on early vs. late surgery for infectious endocarditis (IE) with ICH is conflicting. Changing the cardiopulmonary bypass (CPB) strategy might be necessary to improve the surgical outcomes of IE with ICH. Some studies reported that cardiac surgery using nafamostat mesylate (NM) as an alternative anticoagulant during CPB was performed successfully. The combination of NM and low-dose heparin was beneficial for early surgery in patients with AIE complicated by cerebral infarction and ICH, without worsening cerebral lesions. In this report, we review and discuss the management of CPB in patients with ischemic and hemorrhagic stroke during surgery for AIE.