Clinically distinguishing bipolar disorder (BD) from major depressive disorder (MDD) during depressive states is difficult. Neuroimaging findings suggested that patients with BD and those with MDD differed with respect to the gray matter volumes of their subcortical structures, especially in their striatum. However, whether these disorders have different effects on functionally striatal neuronal activity and connectivity is unclear. Arterial spin labeling and resting-state functional MRI was performed on 25 currently depressive patients with BD, 25 depressive patients with MDD, and 34 healthy controls (HCs). The functional properties of striatal neuronal activity (cerebral blood flow, CBF) and its functional connectivity (FC) were analyzed, and the results from the three groups were compared. The result of the multiple comparisons was corrected on the basis of the Gaussian Random Field theory. The patients with BD and those with MDD both had higher CBF values than the HCs in the right caudate and right putamen. The hyper-metabolism of right striatum in BD patients was associated with increased average duration per depressive episode. The two disorders showed commonly increased FC between the striatum and dorsolateral prefrontal cortex, whereas the altered FC of the striatum with precuneus/cuneus was observed only in patients with BD. Patients with BD and those with MDD had a common deficit in their prefrontal-limbic-striatal circuits. The altered striato-precuneus FC can be considered as a marker for the differentiation of patients with BD from those with MDD.