A manufacturing method of functional film comprising the steps of: a first step of feeding a lengthy substrate with self-support including a first laminate film on a back side, forming an organic film on a front side of the substrate while transferring the substrate, providing a second laminate film on a surface of the organic film, and taking up the substrate into a film roll; and a second step of loading the film roll on a vacuum deposition apparatus, continuously feeding the substrate including the first laminate film and the second laminate film from the film roll, removing the second laminate film while transferring the substrate, forming an inorganic film over the organic film of the substrate, and taking up the substrate into a film roll.