A non-contact type time-domain system for the fluorescence diffuse optical tomography was designed. The system is evaluated by a phantom with a fluorescence target. The contamination of the non-specific scattering superimposed on the excitation profile but it could be reduced with closely locating the detection fiber to the surface (̃1 mm). Next, we analyzed the contamination in the temporal profiles with an Intralipid solution phantom with a fluorescent target. The contamination to the excitation profile is not clearly observed but that to the fluorescence is strong with a short distance between the excitation source and detection. Finally, we have concluded that a larger distance of source and detector yields better fluorescence sensitivity because the background is limiting the fluorescence detection. On the other hand, the signal quality depends on the statistics and thus the optimum range of the distance comes around 30 mm. Finally, this research gives the idea for the design of the source and detection configuration.