When anorexia nervosa (AN) occurs in children below the age of 14 years, it is referred to as early-onset AN (EO-AN). Over the last years, there has been an increased focus on the role of cognitive functioning in the development and maintenance of AN. Adults with AN show inefficiencies in cognitive functions such as flexibility and central coherence. Systematic neuropsychological examinations of patients with EO-AN are missing. Thirty children with EO-AN and 30 adolescents with AN, as well as 60 healthy controls (HC) underwent an extensive neuropsychological examination. ANOVAs with post hoc tests and explorative regression analyses were conducted. Patients with EO-AN (mean age = 2.17 ± 1.57 years) showed no significant differences in flexibility, inhibition, planning, central coherence, visuospatial short- and long-term memory or recognition in comparison to HC (mean age = 11.62 ± 1.29 years). Performance of adolescents with AN (mean age = 15.93 ± 0.70 years) was not significantly different compared to HC (mean age = 16.20 ± 1.26 years). Explorative regression analyses revealed a significant interaction of age and group for flexibility (adjusted R² = 0.30, F = 17.85, p = 0.013, η_p ² = 0.32). Contrary to expectations, the current study could not confirm the presence of inefficient cognitive processing in children with EO-AN compared to HC. Nonetheless, the expected age-related improvement of flexibility might be disrupted in children and adolescents with AN. Longitudinal neuropsychological examinations are necessary to provide more information about the role of cognitive functioning in the development and maintenance of AN.