The deposition of amyloid-β (Aβ) is one of the major pathological hallmarks of Alzheimer's disease (AD), and a higher cholesterol level is involved in the deposition of Aβ. Previous evidence suggested that exercise exerts neuroprotective effects in a variety of AD models. In the present study, we investigated the effects of a 12-week treadmill exercise program on Aβ deposits in amyloid precursor protein (APP)/presenilin 1 (PS1) transgenic mice and the potential underlying mechanism. After 12 weeks of exercise, Aβ deposits were significantly decreased in the hippocampus. Meanwhile, the amyloidogenic pathway of APP metabolism was inhibited, which was associated with a decrease in BACE1 expression. The APP metabolism mediated by the nonamyloidogenic pathway, as indicated by the increase in ADAM10 levels. Coincidentally, exercise reduced the cholesterol level, as evidenced by a significant decrease in the total cholesterol level and the activity of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, as well as a reduction in the number of lipid rafts, as evidenced by a significant decrease in the flotillin 1 level. These finding suggested that the 12-week treadmill exercise program reduced Aβ deposition in the hippocampus of APP/PS1 mice, possibly by regulating ADAM10 and BACE1 levels and by decreasing cholesterol-mediated lipid raft formation, indicating that exercise represents a therapeutic intervention to treat AD.