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Fluorescence molecular tomography (FMT), as a promising imaging modality in preclinical research, can obtain the three-dimensional (3-D) position information of the stem cell in mice. However, because of the ill-posed nature and sensitivity to noise of the inverse problem, it is a challenge to develop a robust reconstruction method, which can accurately locate the stem cells and define the distribution. In this paper, we proposed a sparsity adaptive correntropy matching pursuit (SACMP) method. SACMP method is independent on the noise distribution of measurements and it assigns small weights on severely corrupted entries of data and large weights on clean ones adaptively. These properties make it more suitable for in vivo experiment. To analyze the performance in terms of robustness and practicability of SACMP, we conducted numerical simulation and in vivo mice experiments. The results demonstrated that the SACMP method obtained the highest robustness and accuracy in locating stem cells and depicting stem cell distribution compared with stagewise orthogonal matching pursuit and sparsity adaptive subspace pursuit reconstruction methods. To the best of our knowledge, this is the first study that acquired such accurate and robust FMT distribution reconstruction for stem cell tracking in mice brain. This promotes the application of FMT in locating stem cell and distribution reconstruction in practical mice brain injury models. [ABSTRACT FROM AUTHOR]