Amyloid-β (Aβ) plaque deposition in specific brain regions is a major pathological hallmark of Alzheimer’fs disease (AD). However, the mechanism underlying the regional vulnerability to Aβ deposition in AD is unknown. Herein, we provide evidence that endogenous neuronal activity regulates the regional concentration of interstitial fluid (ISF) Aβ which drives local Aβ aggregation. Using in vivo microdialysis, we show that ISF Aβ levels in multiple brain regions of APP transgenic mice prior to plaque deposition were commensurate with the degree of subsequent plaque deposition and to the concentration of lactate, a marker of neuronal activity. Furthermore, unilateral vibrissae stimulation increased ISF Aβ, and unilateral vibrissae deprivation decreased ISF Aβ and lactate levels in contralateral barrel cortex. Long term unilateral vibrissae deprivation decreased amyloid plaque formation and growth. Our results suggest a mechanism to account for the vulnerability of specific brain regions to Aβ deposition in AD.