Trehalose has been used in the foods, pharmaceuticals, and cosmetics industries due to its multifunctional properties. The aim of this study was to elucidate the effect of trehalose as a partial replacement of sugar on the physicochemical properties of the brown rice tofu during storage. As a result, the L* values for the brown rice tofu without trehalose addition and with the application of 1% trehalose decreased significantly with the passage of the storage day. In contrast, 10% trehalose replacement provided a marked positive effect on the color retention of the brown rice tofu, especially whiteness index, suggesting the prevention of the browning of the brown rice tofu. The water content of the brown rice tofu with incorporation of 10% trehalose was significantly high when compared with other tested brown rice tofu after 7 days of storage, resulting in suppression of the hardening of the brown rice tofu. In addition, the incorporation of trehalose could be suppressed the microbial growth on the brown rice tofu. This study proved that a partial replacement of sugar with trehalose, especially 10% trehalose, could be beneficial on the prevention of the quality degradation and improvement of the shelf life, such as prevention of the browning and suppression of the hardening and microbial growth of the brown rice tofu during storage.