He was the ninth archbishop and seventh cardinal of the See of New York. The sexual abuse cases in Bridgeport would haunt him throughout the decade, and he had to take on old cases in the Archdiocese of New York. The Times pointed out:
Like bishops across the nation, he set up a lay review board to evaluate accusations and make recommendations. The cardinal suspended more than a dozen priests and gave their files to prosecutors, who generally found the cases too old to be prosecuted.
On April 19, 2006, Cardinal Egan participated in the Consistory that elected Pope Benedict XVI. Two years later, he welcomed the Pope to New York, accompanying him to Ground Zero and concelebrating Mass with the Pontiff at Yankee Stadium.
In May of 2009, at the age of 77, Cardinal Egan retired as Archbishop of New York. He maintained and assisted in the works of the archdiocese, while serving on a number of offices of the Vatican.