Scorsese, one of the most influential directors in modern times, already received a Golden Globe earlier this month for his direction of "The Departed." He has been nominated for an Oscar five times, but never won.
Scorsese is joined in the best director category by two-time Oscar winner Clint Eastwood for "Letters from Iwo Jima," Alejandro Gonzalez Innariutu for "Babel," Stephen Frears for "The Queen" and Paul Greengrass for "United 93."
"Letters from Iwo Jima" earned Eastwood a Golden Globe in the foreign film category.
Greengrass' nomination considered a surprise because he was not nominated for either a Golden Globe or the Directors Guild of America nomination, Variety said.
Missing from this category were Bill Condon for "Dreamgirls" and Jonathan Dayton and Valerie Faris for "Little Miss Sunshine." All were nominated for a director's guild award.