The Soft X-ray Spectrometer (SXS) onboard the Hitomi (ASTRO-H) satellite observed several celestial objects. All the observations with the SXS were performed through a beryllium (Be) window installed on the gate-valve of the SXS dewar. However, the Be window had not been well calibrated before launching. Therefore, we measured the transmission of a spare Be window, which is from the same lot as the flight material. The measurements were preformed in 3.8–30 keV range with BL01B1 at SPring-8, and in 2.5–12 keV range combined with BL11B and BL7C at KEK-PF. In this paper, we report mainly the results of the KEK-PF experiment. With the KEK-PF, we measured five places of the Be window. Their estimated thicknesses are consistent with each other within 1.3 μm. In the five transmission data, we confirmed absorption edges by Fe-K, Ni-K and Mn-K and six edge like features at 3460, 6057, 6915, 7590, 8790 and 9193 eV, which can be interpreted as Bragg diffraction by Be polycrystal. By combining the transmissions measured at KEK-PF and at SPring-8, we estimated Be thickness of 259.73±0.01 μm. The amounts of contaminated materials are roughly comparable with the provided values from the provider. We also performed scanning measurements of whole surface in the Be window. In the results, thickness of Be window was found to be uniform in ±1µm from the measurement with 4 keV X-rays.