<b><i>Background:</i></b> Thyroid hormone concentrations may deviate from normal values during critical illness. This condition is known as nonthyroidal illness syndrome (NTIS), and it can influence the results of screening for congenital hypothyroidism (CH) during neonatal extracorporeal membrane oxygenation (ECMO). <b><i>Objectives:</i></b> To determine the incidence of aberrant CH screening results in ECMO-treated neonates, to identify possible determinants, and to follow up patients with abnormal thyroid hormone concentrations. <b><i>Methods:</i></b> In this retrospective cohort study, we included 168 ECMO-treated neonates admitted from 2004 to 2014 and screened by protocol and divided them into the following 3 groups: group 1 (screened during ECMO, n = 107), group 2 (screened shortly before ECMO, n = 26), and group 3 (screened shortly after ECMO, n = 35). <b><i>Results:</i></b> CH screening results were aberrant in 67.3% (72/107) of the neonates screened during ECMO, in 73.1% (19/26) of the neonates screened before ECMO, and in 31.4% (11/35) of the neonates screened after ECMO (p < 0.001). Of the neonates with an aberrant screening result, all but 2 (i.e. 98%) had a low thyroxine concentration with a normal thyrotropin concentration at screening, as is seen in NTIS. None was diagnosed with CH. Mortality did not significantly differ between neonates with an aberrant screening result (32.4%) and neonates with a normal screening result (22.7%; p = 0.18). Screening before ECMO (OR 5.92; 95% CI 1.93-18.20), screening during ECMO (OR 4.49; 95% CI 1.98-10.19), and a higher Pediatric Logistic Organ Dysfunction-2 score (OR 1.31; 95% CI 1.04-1.66) were associated with an aberrant screening result. <b><i>Conclusions:</i></b> Aberrant CH screening results were found in most ECMO-treated neonates screened before or during ECMO, which is likely due to NTIS. Follow-up of thyroid hormone concentrations is best started after recovery from critical illness. Our results suggest that thyroxine therapy is not required during ECMO.