Impairment in cognitive flexibility is a core symptom of anorexia nervosa (AN) and is associated with treatment resistance. Nevertheless, studies on the neural basis of cognitive flexibility in adolescent AN are rare. This study aimed to investigate brain networks underlying cognitive flexibility in adolescents with AN. To address this aim, participants performed a Dimensional Change Card Sorting task during high-density electroencephalography (EEG) recording. Anxiety was measured with the State–Trait Anxiety Inventory. Data were collected on 22 girls with AN and 23 controls. Evoked responses were investigated using global-spatial analysis. Adolescents with AN showed greater overall accuracy, fewer switch trial errors and reduced inverse efficiency switch cost relative to controls, although these effects disappeared after adjusting for trait and state anxiety. EEG results indicated augmented early visual orienting processing (P100) and subsequent impaired attentional mechanisms to task switching (P300b) in subjects with AN. During task switching, diminished activations in subjects with AN were identified in the posterior cingulate, calcarine sulcus and cerebellum, and task repetitions induced diminished activations in a network involving the medial prefrontal cortex, and several posterior regions, compared with controls. No significant associations were found between measures of cognitive flexibility and anxiety in the AN group. Findings of this study suggest atypical neural mechanisms underlying cognitive flexibility in adolescents with AN. More importantly, our findings suggest that different behavioural profiles in AN could relate to differences in anxiety levels. Future research should investigate the efficacy of cognitive training to rebalance brain networks of cognitive flexibility in AN.