Aim of this study consisted in assessing the 24-h heart rate variability (HRV), a measure of autonomic nervous system (ANS) imbalance, in 21 adolescents with functional hypothalamic amenorrhea (FHA, 11 normogonadotropic, N-FHA, and 10 hypogonadotropic, Hy-FHA) compared to 21 patients with anorexia nervosa (AN) and 21 controls. As expected, subjects with AN showed a significant dysregulation in multiple HRV parameters, while Hy-FHA patients presented with a dysregulation in a few domains (SDNN, HFr), which was not present in girls with N-FHA, who showed values largely similar to controls. FHA might represent part of the AN biological spectrum, and a link between these two conditions might exist, possibly related to the degree of psychological and/or hormonal dysfunction.