To ensure the safe geological disposal of radioactive wastes, it is important to determine the permeability of clays. The transient pulse test is suitable to apply to the low permeability materials, because it takes relatively short term to determine the permeability. Usually we increase the upstream pore pressure in the measurement with the transient pulse test. However, it is impossible to determine the permeability of clay in this procedure because of the increase of pore pressure. Therefore, the transient pulse test has never been applied to the determination of permeability of clays. In this study, we tried to apply the transient pulse test to a clay obtained in Mizunami Underground Research Laboratory to determine the permeability with decreasing the downstream pore pressure. It was clarified that the transient pulse test with decreasing downstream pore pressure is appropriate from the measurement of granite. It was shown that the permeability of a clay was determined by the transient pulse test with decreasing the downstream pore pressure, which agreed with the permeability determined from the falling head test. The measurement time of the transient pulse test is much shorter than that of the falling head test. It is concluded that the transient pulse test is appropriate for the determination of the permeability of clays.