We report the crystal structure parameters of clathrate-type copper-oxide Cu6O8YCl, which belongs to the Cu6O8MX (M cation, X anion) family, investigated by the powder neutron diffraction technique and the Rietveld method. The crystal structure of Cu6O8YCl was identified to be a cubic structure with the space group Fmm. The Cl atom is located at the 4a site, which is the center position of the Cu6O8 cage, and the Y atom occupies the 4b site in the cuboid space. The Y and Cl atoms have anomalously large atomic displacement parameters (Uiso) at room temperature, which suggests that Y and Cl atoms respectively present in a cuboid and in a Cu6O8 cage exhibit intensive motion such as rattling, as recently observed for clathrate compounds. © Published under licence by IOP Publishing Ltd.