We evaluated the association of body temperature patterns with neurological outcomes after extracorporeal cardiopulmonary resuscitation (ECPR). Between December 2013 and December 2015, we enrolled 48 patients with cardiac arrest who survived for at least 24 hours after ECPR. Based on their body temperature patterns and the intention to control fever, we divided the patients into those in whom fever was actively controlled (N = 25), those with normothermia (N = 17), and those with unintended hypothermia (N = 6). The primary outcome was the Cerebral Performance Categories (CPC) scale at discharge. Of the 48 ECPR patients, 23 patients (47.9%) had good neurological outcomes (CPC 1 and 2) and 27 patients (56.3%) survived to discharge. The normothermia group showed a pattern of higher temperatures compared with the other groups during 48 hours after ECPR. Not only poor neurological outcomes but also intensive care unit (ICU) mortality occurred more often in the unintended hypothermia group than in the other two groups, regardless of the fever control strategy (p = 0.023 and p = 0.002, respectively). There were no differences in neurological outcomes and ICU mortality between the actively controlled fever group and the normothermia group (p = 0.845 and p = 0.616, respectively). Unintentionally sustained hypothermia may be associated with poor neurological outcomes after ECPR. These findings suggest that patients who are unable to generate a fever following ECPR may incur severe hypoxic brain injury.