According to one embodiment, a blood flow perfusion analyzing apparatus includes tissue and arterial TCC calculation units, first and second making units, a deconvolution unit and a blood flow information calculation unit. The tissue TCC calculation unit obtains tissue TCCs. The arterial TCC calculation unit calculates an arterial TCC. The first making, unit makes first sets, starting from a first time in which elements corresponding to the tissue are arrayed one-dimensionally, based on the tissue TCCs. The second making unit makes a second set, starting from a second time after the first time, in which elements corresponding to the artery are arrayed two-dimensionally, based on the arterial TCC. The deconvolution unit calculates transfer functions of the tissue based on the first and second sets. The blood flow information calculation unit calculates information on a blood flow perfusion based on the transfer functions.