Transcranial magnetic stimulation (TMS) is a noninvasive method for the stimulating brain nerve. Knowing the stimulated brain site in TMS is important to assess the brain function, however it is not easy to identify the stimulating point by TMS so that the induced electric fields is broadly distributed in the brain. Figure-of-eight coil can localize the induced electric field for the target cortical area. We determine the stimulating point by the strength of electric fields. However the nerve excitation property related to the fiber orientation for the induced electric field must be considered. We have proposed a novel method considering the nerve excitation property to estimate the stimulated brain site in TMS. fMRI observed during the motor task enables us to know the motor cortical area precisely. In this study, we measured the cortical area activated during the index and little finger motor task by fMRI and compared the stimulating site innervating the index and little finger muscles estimated by our estimation method. We confirmed the validity of our method for estimation of stimulating sites in TMS by fMRI.