Social anxiety disorder-related alterations in basal ganglia regions, such as striatum and globus pallidus, though evident from metabolic imaging, remain to be explored using seed-based resting-state functional connectivity magnetic resonance imaging. Capitalizing on the enhanced sensitivity of a multichannel array coil, we collected high-resolution (2-mm isotropic) data from medication-naive patients and healthy control participants. Subcortical resting-state networks from structures including the striatum (caudate and putamen), globus pallidus, thalamus, amygdala, and periaqueductal gray were compared between the two groups. When compared with controls, the caudate seed revealed significantly higher functional connectivity (hyper-connectivity) in the patient group in medial frontal, prefrontal (anterior and dorsolateral), orbito-frontal, and anterior cingulate cortices, which are regions that are typically associated with emotional processing. In addition, with the putamen seed, the patient data exhibited increased connectivity in the fronto-parietal regions (executive control network) and subgenual cingulate (affective network). The globus pallidus seed showed significant increases in connectivity in the patient group, primarily in the precuneus, which is part of the default mode network. Significant hyper-connectivity in the precuneus, interior temporal, and parahippocampal cortices was also observed with the thalamus seed in the patient population, when compared with controls. With amygdala as seed region, between-group differences were primarily in supplementary motor area, inferior temporal gyrus, secondary visual cortex, angular gyrus, and cingulate gyrus. Seed from periaqueductal gray resulted in hyper-connectivity in the patient group, when compared with controls, in dorsolateral prefrontal cortex, precuneus, middle temporal gyrus, and inferior parietal lobule. In all the subcortical regions examined in this study, the control group did not have any significant enhancements in functional connectivity when compared with the patient group.