Previously, we showed that chronic administration of 13-cis-retinoic acid (13-cis-RA) induces depression-related behaviors in mice and that 13-cis-RA alters components of the serotonergic system in vitro. Work by others has shown that 13-cis-RA reduces hippocampal neurogenesis in mice and orbitofrontal cortex metabolism in humans. In the current study, we measured cytochrome oxidase activity, a metabolic marker that reflects steady state neuronal energy demand, in various regions of the brain to determine the effects of 13-cis-RA on neuronal metabolic activity and network interactions between the raphe nuclei and the hippocampal system. Brain cytochrome oxidase activity in young adult male mice was analyzed following 6 weeks of daily 13-cis-RA (1 mg/kg) or vehicle injection and behavioral testing. Chronic 13-cis-RA administration significantly decreased cytochrome oxidase activity only in the inferior rostral linear nucleus of the raphe. However, covariance analysis of interregional correlations in cytochrome oxidase activity revealed that 13-cis-RA treatment caused a functional uncoupling between the dorsal raphe nuclei and the hippocampus. Furthermore, a path analysis indicated that a network comprising lateral habenula to dorsal raphe to hippocampus was effectively uncoupled in 13-cis-RA treated animals. Finally, cytochrome oxidase activity in the dentate gyrus of 13-cis-RA treated mice was inversely correlated with depression-related behavior. Taken together, these data show that 13-cis-RA alters raphe metabolism and disrupts functional connectivity between the raphe nuclei and the hippocampal formation, which may contribute to the observed increase in depression-related behaviors.