Heparin has long been a contested therapy in acute ischemic stroke (AIS). In current practice, heparin is considered on a case-by-case basis, but there is no consensus as to the appropriate timing of anticoagulation or for which ischemic stroke subtypes heparin may be beneficial. To provide better clarity on this issue, we review current research focusing on the use of heparin in AIS in each stroke subtype and subsequently make recommendations to provide readers with a systematic approach to managing complex stroke patients for which acute anticoagulation may be valuable. We conclude that there are certain subpopulations of ischemic stroke patients that may derive benefit from heparin when given acutely, including patients with symptomatic large artery stenosis >70 %, non-occlusive intraluminal thrombus, and in patients with high-risk cardiac conditions including left ventricular thrombus, left ventricular assist devices, and mechanical heart valves.