A vacuum processing apparatus for processing a substrate under a vacuum atmosphere includes a vacuum processing module, a vacuum transfer module, a gate valve and a control unit. The vacuum processing module includes a processing chamber, a mounting table and a first gas supply unit. The vacuum transfer module includes a transfer chamber airtightly connected to the processing chamber through the transfer port, a transfer unit and a second gas supply unit. The gate valve is configured to open and close the transfer port for the substrate. The control unit is configured to open the gate valve in a state where a flow rate of an inert gas supplied from the first gas supply unit is smaller than a flow rate of an inert gas supplied from the second gas supply unit and a pressure in the processing chamber is lower than a pressure in the transfer chamber.