Introduction The treatment and outcomes of heparin-induced thrombocytopenia (HIT) are not well described in neurosurgery patients. This study reviewed the treatment for HIT in subarachnoid hemorrhage (SAH) patients, and compared outcomes in patients with isolated HIT (iHIT) and HIT with thrombotic syndrome (HITTS). Methods Adult patients with SAH discharged from the University of Illinois Hospital & Health Sciences System from 2006 to 2009 were included if they had at least one positive HIT antibody test. Patients were categorized with either iHIT or HITTS based on documented evidence of thrombosis. The primary outcome was the incidence of new thromboses prior to discharge. Secondary outcomes included the incidence of major bleeding, new thromboses up to 3 months after discharge, or hospice/death. Patients having any secondary outcome were defined as having a “poor treatment-related effect”. Results A total of 176 patients were screened and 30 patients met inclusion criteria. Eighteen patients (60 %) were categorized with iHIT and 12 (40 %) with HITTS. Twelve patients (67 %) with iHIT received prophylaxis with fondaparinux and nine patients (75 %) with HITTS were treated with argatroban. There were no differences in the primary (11 vs. 25 %, p  = 0.364) or secondary outcomes in the iHIT group versus the HITTS group. Patients with iHIT had a 5.5 % incidence of “poor treatment-related effects” compared to a 33.3 % incidence in patients with HITTS ( p  = 0.024). Conclusions SAH patients with iHIT and HITTS did not differ in the incidence of new thromboses, incidence of hemorrhage, or hospice/death. Patients with iHIT had fewer “poor treatment-related effects” than HITTS patients.