Anorexia Nervosa (AN) is characterized by voluntary food restriction, excessive exercise and mortality rate surpassing that of major depression. Activity-based anorexia (ABA) is an animal model that captures these characteristics of AN, thus having the potential to reveal the neurobiology underlying individual differences in AN vulnerability. Dorsal raphe (DR) is known to regulate feeding but its role in ABA remains unexplored. Through chemogenetic activation, we investigated the role of mPFC pyramidal neurons projecting to DR (mPFC→DR) in an animal’s decision to eat or exercise following ABA induction. Although the DREADD ligand C21 could activate 44% of the mPFC→DR neurons, this did not generate significant group mean difference in the amount of food intake, compared to control ABA mice without chemogenetic activation. However, further analysis of individual animals’ responses to C21 revealed a significant, positive correlation between food intake and mPFC→ DR neurons that co-express cFos, a marker for neuronal activity. cFos expression by GABAergic interneurons (GABA-IN) in mPFC was significantly greater than that for the control ABA mice, indicating recruitment of GABA-IN by mPFC→DR neurons. Electron microscopic immunohistochemistry (EM-ICC) revealed that GABAergic innervation is 60% greater for the PFC→DR neurons than the Layer 5 pyramidal neurons without projections to DR. Moreover, individual differences in this innervation correlated negatively with food intake specifically on the day of C21 administration. We propose that C21 activates two antagonistic pathways: 1) PFC→DR pyramidal neurons that promote food intake; and 2) GABA-IN in the mPFC that dampen food intake through feedback inhibition of mPFC→DR neurons.