Objective: Resting-state functional magnetic resonance imaging (rs-fMRI) studies have revealed inconsistent regional spontaneous neural activity alterations in patients with type 2 diabetes mellitus (T2DM). The aim of our meta-analysis was to identify concordant regional spontaneous neural activity abnormalities in patients with T2DM. Methods: A systematic search was conducted to identify voxel-based rs-fMRI studies comparing T2DM patients with healthy controls. The permutation of subject images seed-based d mapping (SDM) was used to quantitatively estimate the regional spontaneous neural activity abnormalities in patients with T2DM. Metaregression was conducted to examine the associations between clinical characteristics and functional alterations. Results: A total of 16 studies with 19 datasets including 434 patients with T2DM and 391 healthy controls were included. Patients with T2DM showed hypoactivity in the right medial superior frontal gyrus, right superior temporal gyrus, and left lingual gyrus, whereas hyperactivity in the right cerebellum. Metaregression analysis identified negative correlation between regional activity in the medial superior frontal and anterior cingulate gyri and illness duration of patients with T2DM. Conclusion: The patterns of regional spontaneous neural activity alterations, characterized by hypoactivity in the medial pre-frontal cortex, visual cortex, and superior temporal gyrus, whereas hyperactivity in the cerebellum, might represent the underlying neuropathological mechanisms of T2DM.