In 1997, Scorsese received the AFI Life Achievement Award. In 1998, the American Film Institute placed three Scorsese films on their list of the greatest American movies: Raging Bull at #24, Taxi Driver at #47, and Goodfellas at #94. For their tenth-anniversary edition of the list, Raging Bull was moved to #4, Taxi Driver was moved to #52, and Goodfellas was moved to #92.[131] In 2001, the American Film Institute placed two Scorsese films on their list of the most "heart-pounding movies" in American cinema: Taxi Driver at #22 and Raging Bull at #51. At a ceremony in Paris, France, on January 5, 2005, Martin Scorsese was awarded the French Legion of Honour in recognition of his contribution to cinema. On February 8, 2006, at the 48th Annual Grammy Awards, Scorsese was awarded the Grammy Award for Best Long Form Music Video for No Direction Home.

In 2007, Scorsese was listed among Time magazine's 100 Most Influential People in The World.[132] In August 2007, Scorsese was named the second-greatest director of all time in a poll by Total Film magazine, in front of Steven Spielberg and behind Alfred Hitchcock.[133] In 2007, Scorsese was honored by the National Italian American Foundation (N.I.A.F.) at the nonprofit's thirty-second Anniversary Gala. During the ceremony, Scorsese helped launch N.I.A.F.'s Jack Valenti Institute, which provides support to Italian film students in the U.S., in memory of former foundation board member and past president of the Motion Picture Association of America (M.P.A.A.) Jack Valenti. Scorsese received his award from Mary Margaret Valenti, Valenti's widow. Certain pieces of Scorsese's film related material and personal papers are contained in the Wesleyan University Cinema Archives, to which scholars and media experts from around the world may have full access.[134] On September 11, 2007, the Kennedy Center Honors committee, which recognizes career excellence and cultural influence, named Scorsese as one of the honorees for the year. On June 17, 2008, the American Film Institute placed two of Scorsese's films on the AFI's 10 Top 10 list: Raging Bull at #1 for the Sports genre and Goodfellas at #2 for the Gangster genre. In 2013, the staff of Entertainment Weekly voted Mean Streets the seventh greatest film ever made.[135]

On January 17, 2010, at the 67th Golden Globe Awards, Scorsese was the recipient of the Golden Globe Cecil B. DeMille Award. On September 18, 2011, at the 63rd Primetime Emmy Awards, Scorsese won the Primetime Emmy Award for Outstanding Directing for a Drama Series for his work on the series premiere of Boardwalk Empire. In 2011, Scorsese received an honorary doctorate from the National Film School in Lodz. At the awards ceremony he said, "I feel like I'm a part of this school and that I attended it," paying tribute to the films of Wajda, Munk, Has, Polanski and Skolimowski.[136] King Missile wrote "Martin Scorsese" in his honor. On February 12, 2012, at the 65th British Academy Film Awards, Scorsese was the recipient of the BAFTA Academy Fellowship Award. 

On September 16, 2012, Scorsese won two Emmy Awards for Outstanding Directing for Nonfiction Programming and Outstanding Nonfiction Special for his work on the documentary George Harrison: Living in the Material World.[137] In 2013, the National Endowment for the Humanities selected Scorsese for the Jefferson Lecture, the U.S. federal government's highest honor for achievement in the humanities. He was the first filmmaker chosen for the honor.[138] His lecture, delivered on April 1, 2013, at the John F. Kennedy Center for the Performing Arts was titled "Persistence of Vision: Reading the Language of Cinema".[139] Martin Scorsese was awarded the Polish Gold Medal for Merit to Culture – Gloria Artis on April 11, 2017, in recognition of his contribution to Polish cinema.[140] 

Scorsese has also garnered favorable responses from numerous film giants, who include Ingmar Bergman,[141] Frank Capra,[142] Jean-Luc Godard,[143] Werner Herzog,[144] Elia Kazan,[145] Akira Kurosawa,[146] David Lean,[147] Michael Powell,[148] Satyajit Ray,[149] and François Truffaut.[150] He was awarded an Honorary Doctorate from the University of Oxford on June 20, 2018.[151]