In this paper, we demonstrate a method using a frequency comb, which can precisely measure the refractive index of water. We have developed a simple system, in which a Michelson interferometer is placed into a quartz-glass container with a low expansion coefficient, and for which compensation of the thermal expansion of the water container is not required. By scanning a mirror on a moving stage, a pair of cross-correlation patterns can be generated. We can obtain the length information via these cross-correlation patterns, with or without water in the container. The refractive index of water can be measured by the resulting lengths. Long-term experimental results show that our method can measure the refractive index of water with a high degree of accuracy—measurement uncertainty at 10⁻⁵ level has been achieved, compared with the values calculated by the empirical formula.