Neuropsychological sequelae have been reported in adults with anorexia nervosa (AN). However, there is dearth of investigations examining neuropsychological functioning in youths with eating disorders. More critically, as a result of its status as a new psychiatric diagnosis under DSM-5, there are no published empirical studies to date investigating the neuropsychological profiles of youths with avoidant/restrictive food intake disorder (ARFID). We examined neuropsychological similarities and differences in youth with AN and ARFID and their correlation with age, weight, comorbidities, and eating pathology. Children and adolescents with AN and ARFID from an eating disorders clinic (N = 28) participated in this cross-sectional, exploratory study. Independent sample t-tests, Pearson’s correlations, and Bonferroni corrections were used to investigate group differences and associations among variables under investigation. Participants with ARFID demonstrated lower intellectual ability and relatively greater set-shifting difficulties/cognitive inflexibility. Group differences did not emerge in visuospatial abilities, central coherence, processing speed, attention, or memory. Same age comparisons did not yield any gender differences in central coherence. Positive correlations between Full Scale IQ and some neuropsychological tasks were observed in the AN but not in the ARFID group. Weight and neuropsychological functioning were not correlated. Given the relative similarities in neuropsychological profiles between AN and ARFID, it is critical that future studies should evaluate the progression in neuropsychological profiles to identify risk factors for progression to AN across developmental stages and examine the impact of malnutrition rather than weight. Longitudinal studies combining neuropsychological assessment with functional neuroimaging are necessary to identify target brain regions that may hold promise for psychopharmacological and psychotherapeutic interventions.