A plasma processing apparatus that performs plasma processing to a substrate held on a transport carrier including a frame and a holding sheet that covers an opening of the frame includes: a transport mechanism that transports the transport carrier; a position measuring section that measures a position of the substrate to the frame; a plasma processing section that includes a plasma processing stage on which the transport carrier is loaded and a cover that covers the frame and a part of the holding sheet loaded on the plasma processing stage, and has a window section for exposing a part of the substrate; and a control section that controls the transport mechanism such that the transport carrier is loaded on the plasma processing stage to satisfy a positional relationship between the window section and the substrate based on the position information of the substrate to the frame.