In June 1960, Kelley joined the United States Navy through the Officer Candidate School program in Newport, Rhode Island. After assignments as a surface warfare officer on and, he volunteered for service in Vietnam as a lieutenant in command of River Assault Division 152, part of the Mobile Riverine Force. On June 15, 1969, Kelley led eight river assault craft boats on a mission to extract a United States Armyinfantry company from the bank of the Ong Muong Canal in Kien Hoa Province, South Vietnam. When a boat malfunctioned, he ordered the other craft to circle the disabled boat that had come under attack and placed his boat directly in the line of enemy fire. A rocket-propelled grenade struck nearby, severely injuring Kelley, but he continued to protect his men until they could get to safety, then ordered medical assistance for himself. For this feat he was awarded the Medal of Honor. Despite the loss of one eye during this action and the navy's decision that he was no longer fit for service, Kelley persevered in his requests to remain on active duty. Kelley's following seagoing assignments included that of executive officer of and commanding officer of, which deployed to the South China Sea in 1978 to rescue refugees from Vietnam, then to the Philippines as well as South Korea. In addition, he earned his master's degree in management at the Naval Postgraduate School in Monterey, California. Later he completed the Armed Forces Staff College course in Norfolk, Virginia, and served in the Office of the Chief of Naval Operations in manpower and planning. In 1982, Kelley was assigned to Yokohama as the commander of the navy's Military Sealift Command Far East for oversight of its ships' repairs and maintenance. His following assignment was as chief of staff for the commander of United States Naval Forces in Korea. Kelley's final assignment was as the director of legislation in the Bureau of Naval Personnel. There he worked closely with Vice Admiral Mike Boorda in enhancing the responsibilities and stature of enlisted personnel, while closely integrating minorities and women into mainstream assignments. He retired in 1990.
Later and current life
After his navy service, Kelley worked as a civilian in the Department of Defense for several years before returning to Boston. He became commissioner of the Massachusetts Department of Veterans' Services in April 1999 and was named Secretary of that department in August 2003. While Secretary, Kelley ran the Commonwealth's veterans' public assistance program, along with educational benefits and annuities for the disabled. After 9/11, as veterans began returning to Massachusetts, Kelley instituted new programs to reach their unique needs, especially those involving the unseen wounds of war, such as traumatic brain injury and suicide prevention. He hired young, disabled veterans for better outreach to this new cadre. He also worked with the United States Department of Labor to enforce federal employment protections for returning service men and women. In January 2011, Kelley retired from public service. His combined forty-plus years of naval and state service were recognized in a retirement party attended by 500 persons that also raised $300,000 for the Massachusetts Soldiers' Legacy Fund, which pays the educational expenses for children of those soldiers who died in the Global War on Terror. As president of the Medal of Honor Society, Kelley advocates for the living recipients and their spouses and promotes their Character Development Program in middle, high, and now elementary schools. The program draws on examples of courage, commitment, sacrifice and integrity from the recipients' own lives. Kelley also provides meals for a homeless shelter and helps run the veterans' ministry at his church. He remains close to Holy Cross and serves on its O'Callahan Society that supports the NROTC program there. He mentors students at B.C. High and is an active alumnus.
Kelley has three daughters, Liza DuVal, Kate Clark and Jane Kelley. Kelley married the former Joan O'Connor in October 2005. She retired from the Navy Reserves as a commander after twenty years as a public affairs officer.