Brain volume loss, or atrophy, has been proven to be an important characteristic of neurological diseases such as Alzheimer's disease and multiple sclerosis. To use atrophy rate as a reliable clinical biomarker and to increase statistical power in clinical treatment trials, measurement variability needs to be minimized. Among other sources, systematic differences between different MR scanners are suspected to contribute to this variability. In this study we developed and performed initial validation tests of an MR-compatible phantom and analysis software for robust and reliable evaluation of the brain volume loss. The phantom contained three inflatable models of brain structures, i.e. cerebral hemisphere, putamen, and caudate nucleus. Software to reliably quantify volumes form the phantom images was also developed. To validate the method, the phantom was imaged using 3D T1-weighted protocols at three clinical 3T MR scanners from different vendors. Calculated volume change from MRI was compared with the known applied volume change using ICC and mean absolute difference. As assessed by the ICC, the agreement between our developed software and the applied volume change for different structures ranged from 0.999–1 for hemisphere, 0.976–0.998 for putamen, and 0.985–0.999 for caudate nucleus. The mean absolute differences between measured and applied volume change were 109–332 μL for hemisphere, 2.9–11.9 μL for putamen, and 2.2–10.1 μL for caudate nucleus. This method offers a reliable and robust measurement of volume change using MR images and could potentially be used to standardize clinical measurement of atrophy rates.