The Neogene elevation history of the Mount Everest region is key for understanding the tectonic history of the world’s highest mountain range, the evolution of the Tibetan Plateau, and climate patterns in East and Central Asia. In the absence of fossil surface deposits such as paleosols, volcanic ashes, or lake sediments, we conducted stable isotope paleoaltimetry based on the hydrogen isotope ratios (δD) of hydrous minerals that were deformed in the South Tibetan detachment shear zone during the late Early Miocene. These minerals exchanged isotopically at high temperature with meteoric water (δDwater = −156‰ ± 5‰) that originated as high-elevation precipitation and infiltrated the crustal hydrologic system at the time of detachment activity. When compared to age-equivalent near-sea-level foreland oxygen isotope (δ18O) paleosol records (δ18Owater = −5.8‰ ± 1.0‰), the difference in δ18Owater is consistent with mean elevations of ≥5000 m for the Mount Everest area. Mean elevations similar to modern suggest that an early Himalayan rain shadow may have influenced the late Early Miocene climatic and rainfall history to the north of the Himalayan chain.