Aerobic exercise (AE) has recently received increasing attention in the prevention of Alzheimer’s disease (AD). There is some evidence that it can improve neurocognitive function in elderly individuals. However, the mechanism of these improvements is not completely understood. In this prospective clinical trial, thirty amnestic mild cognitive impairment participants were enrolled into two groups and underwent 12 months of intervention. One group (n = 15) performed AE training (8M/7F, age = 66.4 years), whereas the other (n = 15) performed stretch training (8M/7F, age = 66.1 years) as a control intervention. Both groups performed 25–30 minutes training, 3 times per week. Frequency and duration were gradually increasedovertime.Twelve-monthAEtrainingimprovedcardiorespiratoryfitness(p = 0.04)andmemoryfunction(p = 0.004). Cerebral blood flow (CBF) was measured at pre- and post-training using pseudo-continuous-arterial-spin-labeling MRI. Relative to the stretch group, the AE group displayed a training-related increase in CBF in the anterior cingulate cortex (p = 0.016). Furthermore, across individuals, the extent of memory improvement was associated with CBF increases in anterior cingulate cortex and adjacent prefrontal cortex (voxel-wise p < 0.05). In contrast, AE resulted in a decrease in CBF of the posterior cingulate cortex, when compared to the stretch group (p = 0.01). These results suggest that salutary effects of AE in AD may be mediated by redistribution of blood flow and neural activity in AD-sensitive regions of brain.