Introduction: Diabetes mellitus (DM) is one of the major chronic diseases, which enhances the risk of erectile dysfunction (ED). However, the central pathological mechanisms of ED in DM patients are still unclear. Methods: Resting-state functional magnetic resonance imaging (rs-fMRI) data were acquired in 30 type-2 diabetes mellitus (T2DM), 31 T2DM with ED (DM-ED) patients and 30 healthy controls (HCs). The measure of fractional amplitude of low-frequency fluctuation (fALFF) was calculated and compared among groups. Results: Differences of fALFF values were found in the left superior frontal gyrus (medial) and middle temporal gyrus among three groups. Compared with HCs group, T2DM group exhibited lower fALFF values in the left superior frontal gyrus (dorsolateral), anterior cingulate gyrus, calcarine fissure and increased fALFF values in the left postcentral gyrus. Compared with HCs group, DM-ED group exhibited lower fALFF values in the left superior frontal gyrus (medial), middle temporal gyrus, temporal middle (pole) and increased fALFF values in the right postcentral gyrus. Compared with T2DM group, DM-ED group exhibited increased fALFF values in the right median cingulum gyrus and left calcarine fissure. Conclusion: DM-ED patients showed functional changes in brain regions that were closely correlated with sexual dysfunction, which suggested that altered regional brain activity might be related to the pathophysiology of DM-ED.