Kelly was the first person to rise from Police Cadet to Police Commissioner, holding all of the department's ranks, except for Three-Star Bureau Chief, Chief of Department, and Deputy Commissioner, having been promoted directly from Two-Star Chief to First Deputy Commissioner in 1990. After his handling of the World Trade Center bombing in 1993, he was mentioned for the first time as a possible candidate for FBI Director. After Kelly turned down the position, Louis Freeh was appointed.

Kelly was a Marine Corps Reserve Colonel, Director of Police under the United Nations Mission in Haiti, and an Interpol Vice President. During the Clinton administration, Kelly served as Treasury Department Under Secretary for Enforcement, as Customs Service Commissioner, and was in the running to become the first United States Ambassador to Vietnam, after President Bill Clinton extended full diplomatic relations to that country in 1995.

Kelly is the recipient of honorary degrees from Marist College, Manhattan College, the College of St. Rose, St. John's University, the State University of New York, New York University, Iona College, Pace University, Quinnipiac University, St. Thomas Aquinas College and the Catholic University of America.