Background <p>The raphe nuclei, the principal sources of serotonergic projections, are central to emotional processing and reward regulation. Since altered raphe nucleus function is implicated in depression, we mapped voxel-based functional connectivity (FC) of the dorsal (DRN) and medial raphe nucleus (MRN). This study aimed to investigate FC alterations in depressed adolescents, to determine their associations with clinical symptoms, and to evaluate the potential of these FC metrics to identify adolescents with depression using a support vector machine (SVM).</p> Method <p>We recruited 102 patients with depression and 54 healthy controls matched for age and sex. FC of the DRN and MRN was assessed. Associations between FC measures and clinical questionnaire scores were examined. The classification performance of different feature combinations, which were based on significant FC features, was evaluated using an SVM.</p> Results <p>Patients showed increased FC between the DRN and the left precentral gyrus, whereas decreased FC was observed between the MRN and several regions, including the right gyrus rectus, the left nucleus accumbens, and the right putamen. FC between the MRN and the right gyrus rectus was positively associated with suicidal ideation (<i>r</i> = 0.221), although this finding did not remain significant after multiple comparison correction. Additionally, SVM analysis demonstrated the optimal combination of FC features from the left precentral gyrus, and the right gyrus rectus could effectively discriminate depressed adolescents.</p> Conclusion <p>Our findings demonstrate dysregulation in raphe nucleus subregions that show abnormal connectivity with related brain areas. Such alterations may contribute to the pathophysiology of adolescent depression and suggest potential novel candidate connectivity features for its clinical assessment.</p>