An apparatus for manufacturing a magnetic recording disk includes a magnetic-film deposition chamber in which a magnetic film for a recording layer is deposited on a substrate; a lubricant-layer preparation chamber in which a lubricant layer is prepared on the substrate in vacuum; and a cleaning chamber in which the substrate is cleaned in vacuum after the magnetic-film deposition in the magnetic-film chamber and before the lubricant-layer preparation in the lubricant-layer chamber. The apparatus may further include a transfer system that transfers the substrate from the cleaning chamber to the lubricant-layer preparation chamber without exposing the substrate to the atmosphere.