Background The aim of this study was to investigate whether intermittent electroencephalography (EEG) could be used to predict neurological prognosis of patients who underwent extracorporeal cardiopulmonary resuscitation (ECPR). Methods This was a retrospective, single center, and observational study of adult patients who were evaluated by EEG scan within 96 hours after ECPR between February 2012 and December 2018. The primary endpoint was neurological status upon discharge from the hospital assessed with Cerebral Performance Categories (CPC) scale. Results Among 69 adult cardiac arrest patients who underwent ECPR, 32 (46.4%) patients survived until discharge from the hospital. Of these 32 survivors, 17 (24.6%) patients had favorable neurological outcomes (CPC score: 1 or 2). Sedatives or analgesics were used in 41 (59.4%) patients. Malignant EEG patterns were more common in patients with poor neurological outcome than in patients with favorable neurological outcome (73.1% vs. 5.9%, p < 0.001). All patients with highly malignant EEG patterns (43.5%) had poor neurological outcome. Moderately malignant EEG patterns were reported in 8 (11.6%) patients with poor neurological outcome and one (1.4%) patient with favorable neurological outcome. Benign EEG patterns were more common in patients with favorable neurological outcome than in patients with poor neurological outcome (94.1% vs. 26.9%, p < 0.001). In multivariable analysis, malignant EEG patterns (adjusted odd ratio [OR]: 53.26, 95% confidence interval [CI]: 5.956 – 476.249) and duration of cardiopulmonary resuscitation (adjusted OR: 1.07, 95% CI: 1.011 – 1.130) were significantly associated with poor neurological outcomes in patients who underwent ECPR (Hosmer-Lemeshow Chi-squared = 7.84, df = 7, p = 0.347). Conclusions In this study, malignant EEG patterns within 96 hr after cardiac arrest were significantly associated with poor neurological outcomes in patients who underwent ECPR. Therefore, early intermittent EEG scan could be helpful for predicting neurological prognosis of post-cardiac arrest patients after ECPR.