The refraction of fluorescence from the inside of a sample at the surface results in fluctuations in fluorescence computed tomography (CT). We evaluated the influence of the difference in refractive index (RI) between the sample body and the surroundings on fluorescence CT results. The brightest fluorescent point is away from the correct point on the tomograms owing to the refraction. The speculated position is determined as the exact point if the RI ratio ranges between 0.97 and 1.03 by immersing the body in an RI matching liquid. The results can help in experimental settings of fluorescence CT for acquiring three-dimensional positional information.