To date, the course of cognitive development in children after liver transplantation (Ltx) is poorly understood. Cognitive performance, however, is crucial in all developmental stages and for educational achievement. This cross‐sectional single‐center study examined the prevalence of long‐term cognitive impairment in a cohort of 64 pediatric patients after Ltx. Median age at Ltx was 12 months. The revised Wechsler Intelligence Scale IV was administered to assess cognitive performance. Patients were compared with an age‐ and gender‐matched group of children without a chronic health condition. Liver transplanted children performed significantly worse in three of four cognitive domains as well as in the Total Intelligence Quotient (Total IQ) (p = 0.017 to p = 0.005). Liver transplant recipients showed substantially more “serious delays” (IQ < 70) compared to the reference group (9.4% vs. 4.7%). Children with a genetic–metabolic disease performed worse than the other groups in three of the four WISC Indices and in the Total IQ (p = 0.05 to p = 0.01). The strongest association was revealed between height at Ltx and Verbal Comprehension (R2 = 0.21), Perceptual Reasoning (R2 = 0.30), Working Memory (R2 = 0.23) and Total IQ (R2 = 0.25). Our results indicate a high impact of primary diagnosis and height percentile at Ltx even on children's long‐term cognitive performance.