An increasing empirical evidence supports a relationship between autism spectrum disorder (ASD) and anorexia. Higher autistic traits are reported in anorexia and a subgroup of adolescent females with anorectic symptomatology could receive an ASD categorial diagnosis. In this case report of a 12-year-old female, we present clinical challenges in the recognition and diagnosis of ASD during hospitalization for anorectic symptomatology: ASD assessment during hospitalization did not support the diagnosis, while another ASD assessment one year later supported the diagnosis, reflecting a changing clinical picture in comparison with that predominant during the anorectic period. In conclusion, the phase of illness and the setting of assessment may influence the detection of a suspected underlying ASD in presence of an acute anorectic symptomatology.