The Medical Internal Radiation Dosimetry (MIRD) method assumes that the beta particle energy is absorbed completely in the source organ. However, the organs of mice used in fundamental experiments for internal radiotherapy are relatively small compared to the range of high-energy ⁹⁰Y beta particles. Therefore, it is well known that the high-energy beta particle can escape the source organ, resulting in large cross-organ doses. The more realistic geometric model such as a voxel-phantom based on Computed Tomography scans for a mouse has been needed for accurately estimating internal doses from administered beta particle emitters. Then it becomes important to simulate the beta particle transport precisely using the Monte Carlo code. The purpose of this study is to validate a user code to simulate the beta particle transport in a mouse in the Monte Carlo code system (EGS5) by comparing with the absorbed dose measured using a number of small fluorescent glass dosimeters and one capsule of ⁹⁰YCl₃ solution implanted in a small tough-water phantom simulating a mouse. It was found that the absorbed dose distribution in this phantom calculated with this user code gave rather good agreement with the measured results.