Rats exposed to timed restricted meals develop anticipation of food. They increase their activity levels in the hours preceding food access; this has been described as food-anticipatory activity (FAA). In the present study, we show the involvement of regions of the hypothalamus [arcuate nucleus, dorsomedial hypothalamus (DMH) and lateral hypothalamus] in the early development of FAA in rats exposed to the activity-based anorexia (ABA) model. We thereby used two different paradigms, rats exposed to the ABA model (ABA-normal) and rats exposed to the same restraint in food access but on a random feeding schedule (ABA-random). The latter group of rats were not able to anticipate food. We found a strong correlation between the expression of food anticipation measured by running-wheel activity and Fos expression levels in the DMH of ABA-normal rats, whereas no correlation was found in ABA-random rats. In contrast, in the randomly fed ABA rats only, a strong negative correlation was found between the neuronal activity in the hypothalamic area and the percentage body weight loss. Interestingly, these results imply that anticipation of meals during food restriction more strongly affects activation in the hypothalamus than negative energy balance alone. We conclude that during the early stages of development of FAA, the DMH plays a role in anticipation of food during periods of negative energy balance.