We investigated the effects of an artificial menstrual cycle on brain structure and activity in young women using metabolic magnetic resonance imaging (MRI). We show that the activation of the hypothalamo-pituitary-gonadal axis during the pill-free interval of low-dose combined oral contraceptive use is associated with transient microstructural and metabolic changes in the female hypothalamus but not in the thalamus, a brain structure unrelated to reproductive control, as assessed by water diffusion and proton magnetic resonance spectra measurements. Our results provide neuroanatomical insights into the mechanism by which sex steroid hormones mediate their central effects and raise the intriguing possibility that specific regions of the neuroendocrine brain use ovarian cycle-dependent plasticity to control reproduction in humans. These MRI-based physiological studies may pave the way for the development of new diagnostic and treatment strategies in the central loss of reproductive competence in human syndromes, such as hypothalamic amenorrhea.