The subgenual anterior cingulate cortex (sgACC) presents altered functional connections with other regions of the brain in individuals with depression. However, the developmental nature of this phenomenon remains largely unexplored. Functional connections of the sgACC were examined in 36 school age children, 17 with a history of preschool onset major depressive disorder (PO-MDD). The sgACC exhibited increased connections with cognitive control regions in healthy children and increased connections with thalamic and parietal regions in the PO-MDD group. A significant correlation between dysregulated emotional behavior and connectivity of the sgACC and dorsal medial prefrontal cortex was also found. These findings demonstrate that atypical sgACC functional connections are evident as early as school age in children with a history of PO-MDD and suggest an association with a very early episode of depression.