A highly-sensitive pharmacokinetic diffuse fluorescence tomographic system is proposed to achieve the indocyanine green (ICG) pharmacokinetic imaging of small animals. The system employs a photon-counting technique based on discrete optical fiber measurement of computed tomography scanning mode in the computer tomography, which effectively improves spatial sampling resolution of the system on the premise of high sensitivity and wide dynamic measurement range. Meanwhile, it adopts serial-parallel mixed measurement mode through switching four photomultiplier tube photon-counting channels by optical switch to obtain a balance between time resolution of measurement and cost-effectiveness of the system. We investigate the principle validity of the system by designing a dynamic phantom that can simulate ICG metabolism in living tissue. In addition, combined with the algorithm of fluorescent agent pharmacokinetic imaging developed by our laboratory, the reconstruction of ICG metabolic velocity is realized. Experimental results show that the proposed system has high sensitivity, spatial resolution and quantitativeness.