The movie, about Jesuit missionaries in 17th-century Japan, was screened this week in Rome.
The pontiff told Scorsese he had read the book on which the film is based.
It was a "very cordial" meeting, the Vatican said.
Pope Francis is a Jesuit who joined the order while he was a young man in Argentina with the idea of becoming a missionary in Japan. But health problems scuttled that dream.
Pope Francis thanked Scorsese for his gift of two paintings.
The work of an 18th-century Japanese artist, the paintings served as a reference for some of the details in the film.
