The "Hugo" director will get financial back-up from Emmett/Furla Films to make the film, which is planned to shoot in Taiwan, reported Ace Showbiz.
The novel, which is titled "Chinmoku" in Japanese, centers on 17th century Jesuits who puts their lives at risk to spread Christianity in Japan.
Scorsese, 70, has voiced his interest in making "Silence" since 1991 and, at that time, Benicio del Toro and Daniel Day-Lewis were attached to star in the film.
The filmmaker will start focusing on his new project after completing "The Wolf of Wall Street", which stars Leonardo DiCaprio.