To analyze the risk factors for intracranial hemorrhage (ICH) in congenital heart disease (CHD) patients supported with venoarterial extracorporeal membrane oxygenation (VA-ECMO). We performed a retrospective analysis of VA ECMO patients after open heart surgery in Shanghai Children’s Medical Center from February 2017 to December 2018, with a total of 50 patients: 14 patients in the ICH group and 36 patients in the control group. Clinical data were analyzed and compared between groups to search for risk factors for ICH. The overall incidence of ICH was 28% (14/50). The in-hospital mortality rate of the ICH group was 57.1% (8/14) vs. 58.3% (21/36) in the control group. The proportion of neonates in the ICH group was 64.3% (9/14) vs. 25% in the control group (9/36) (p = 0.009), and the ICH incidence in extracorporeal cardiopulmonary resuscitation (ECPR) patients was 64.3% (9/14) vs. 13.9% (5/36) (p = 0.000). The percentage of selective cerebral perfusion in the ICH group was 64.3% (9/14) vs. 16.7% (6/36) (p = 0.001) in the control group, and the maximum procalcitonin (PCT) was 43.70 ± 30.48 ng/ml in the ICH group versus 26.92 ± 23.28 ng/ml (p = 0.050) in the control group. Multivariate analysis showed that neonates (odds ratio [OR] = 6.47 [1.09–38.46]), ECPR use (OR = 7.48 [1.26–44.41]), and maximum PCT values (OR = 1.04 [1.001–1.070]) were independent risk factors for ICH. The probability of ICH remains high in children supported with VA-ECMO after cardiac surgery. Neonatal patients, ECPR use, and PCT peak values are independent risk factors for ICH.