General Kelly was born and raised in Boston, MA. He enlisted in the Marine Corps in 1970, and was discharged as a sergeant in 1972, after serving in an infantry company with the 2nd Marine Division, Camp Lejeune, NC. Following graduation from the University of Massachusetts in 1976, he was commissioned and returned to the 2nd Marine Division where he served as a rifle and weapons platoon commander, company executive officer, assistant operations officer, and infantry company commander. Sea duty in Mayport, FL, followed, at which time he served aboard aircraft carriers USS Forrestal and USS Independence. In 1980, then Captain Kelly transferred to the U.S. Army's Infantry Officer Advanced Course in Fort Benning, GA. After graduation, he was assigned to Headquarters Marine Corps, Washington, DC, serving there from 1981 through 1984, as an assignment monitor. Captain Kelly returned to the 2nd Marine Division in 1984, to command a rifle and weapons company. Promoted to the rank of Major in 1987, he served as the battalion's operations officer.
In 1987, Major Kelly transferred to the Basic School, Quantico, VA, serving first as the head of the Offensive Tactics Section, Tactics Group, and later assuming the duties of the Director of the Infantry Officer Course. After three years of instructing young officers, he attended the Marine Corps Command and Staff College, and the School for Advanced Warfare, both located at Quantico. Completing duty under instruction and selected for Lieutenant Colonel, he was assigned as Commanding Officer, 1st Light Armored Reconnaissance Battalion, 1st Marine Division, Camp Pendleton, CA. Holding this command position for two years, Lieutenant Colonel Kelly returned to the East Coast in 1994, to attend the National War College in Washington, DC. He graduated in 1995, and was selected to serve as the Commandant's Liaison Officer to the U.S. House of Representatives, Capitol Hill, where he was promoted to the rank of Colonel.
In 1999, Colonel Kelly transferred to joint duty and served as the Special Assistant to the Supreme Allied Commander, Europe, in Mons, Belgium. He returned to the United States in 2001, and was assigned to a third tour of duty at Camp Lejeune, now as the Assistant Chief of Staff G-3 with the 2nd Marine Division. In 2002, selected to the rank of Brigadier General, Colonel Kelly again served with the 1st Marine Division, this time as the Assistant Division Commander. Much of Brigadier General Kelly's two-year assignment was spent deployed in Iraq. He then returned to Headquarters Marine Corps as the Legislative Assistant to the Commandant from 2004 to 2007. Promoted to major general, he returned to Camp Pendleton as the Commanding General, I Marine Expeditionary Force (Forward). The command deployed to Iraq in early 2008 for a year-long mission, replacing II Marine Expeditionary Force (Forward) as Multinational Force-West in Al Anbar and western Ninewa provinces. General Kelly commanded Marine Forces Reserve and Marine Forces North from October 2009 to March 2011. General Kelly comes to United States Southern Command from his previous position as the Senior Military Assistant to the Secretary of Defense from March 2011 to October 2012.