Children with congenital anatomical foregut anomalies and children treated with neonatal extracorporeal membrane oxygenation (ECMO) are at risk for neurocognitive morbidities. We evaluated the association between the parent-reported pediatric perceived cognitive functioning (PedsPCF) questionnaire and the parent-reported behavior rating inventory of executive function (BRIEF) as well as neuropsychological assessments (NPA). We included 8-, 12- and 17-year-old participants who had joined a prospective follow-up program between 2017 and 2019. Self- and parental proxy-reported PedsPCF and proxy-reported BRIEF scores and their mutual association were evaluated. In total, 168 participants were included. Self- and proxy-reported PedsPCF scores were significantly below normal (mean (SD) z-score: −0.35 (0.88), p < 0.001; −0.36 (1.06), p < 0.001, respectively). Total BRIEF scores were significantly above normal (mean (SD) z-score 0.33 (0.98), p < 0.001). Proxy-reported PedsPCF scores and the Metacognition Index subscores of the BRIEF correlated strongly (τ = 0.551, p < 0.001). Self-reported PedsPCF scores were not associated with NPA test scores. Proxy-reported PedsPCF scores were positively associated with multiple NPA test scores, especially intelligence (R2 = 0.141). The proxy-reported PedsPCF revealed cognitive problems more often than the BRIEF in school-aged children who had survived neonatal critical illness. The proxy-reported PedsPCF may support clinical decision-making regarding the need for extensive neuropsychological assessments.