We studied the effect of deuteration on the relaxation dynamics of the excimer of perylene in solution using subnanosecond time-resolved transient absorption spectroscopy based on the randomly interleaved pulse-train method. We found that the deuterated perylene excimer in solution had a longer lifetime than the undeuterated excimer but that deuteration had a little effect on the ground-state and transient absorption spectra of the excimer, suggesting that deuteration altered the relaxation dynamics by inducing small changes in vibrational properties. To confirm the origin of the deuteration effect, we quantitatively analyzed the kinetics of transient absorption decay, including the decay of triplet-triplet absorption. In addition, we evaluated the effects of temperature on the lifetime of the excimers. On the basis of these results, we concluded that the rate of internal conversion was suppressed by deuteration. By comparing our results with previously reported results on the effect of deuteration on the fluorescence properties of crystalline perylene, we proposed a model that may explain the effect of deuteration on the lifetime of the perylene excimer in solution.