Scorsese, 74, was accompanied by his wife, his two daughters, the producer of the movie for the meeting yesterday, according to a Vatican statement that said the meeting was "very cordial" and lasted 15 minutes.
Pope Francis told those present that he had read Japanese author Shusaku Endo's novel on which the film was based.
Scorsese gave the Pope two paintings on the theme of "hidden Christians," one of them a much-venerated image of the Madonna painted by a 17th century Japanese artist. Pope Francis gave his guests rosaries.
The movie is due to premiere in the United States this December.