Recent advances in genetic neuromodulation technology have enabled circuit-specific interventions in nonhuman primates (NHPs), thereby revealing the causal functions of specific neural circuits. Going forward, an important step is to use these findings to better understand neuropsychiatric and neurological disorders in humans, in which alterations in functional connectivity between brain regions are demonstrated. We recently identified the causal roles of the pathways from the dorsolateral prefrontal cortex (DLPFC) to the lateral part of the mediodorsal thalamic nucleus (MDl) and dorsal caudate nucleus (dCD) in working memory and decision-making, respectively. In the present study, we examined the resting-state functional connectivity of these two prefronto-subcortical circuits in healthy controls (HCs) and patients with various neuropsychiatric disorders including schizophrenia (SCZ), major depressive disorder (MDD), and autism spectrum disorders (ASD) in humans. We found that the functional connectivity of two pathways, DLPFC-MDl and DLPFC-dCD, was significantly reduced in the SCZ groups compared to HCs; however, this hypoconnectivity was not observed in the ASD or MDD groups, suggesting a disease-specific profile of altered prefronto-subcortical connectivity at rest. These results suggest that causal findings of pathway-specific functions revealed in NHPs can be effectively translated to identify the altered connectivity in neuropsychiatric disorders with related symptoms in humans.