Lieutenant General Flynn graduated from the United States Naval Academy in 1975. He holds a Master of Arts Degree in International Relations from Salve Regina College, a Master of Arts Degree in National Security and Strategic Studies from the Naval War College, and a Master of Science Degree in National Security and Strategy from the National War College. He is a Distinguished Graduate of the College of Naval Command and Staff and the National War College.

Lieutenant General Flynn's command assignments include: Commanding Officer, HQ Battery, 2nd Battalion, 12th Marines; (1979-1980); Commanding Officer, L Battery, 2nd Battalion, 12th Marines (1980); Commanding Officer, P Battery, 5th Battalion, 10th Marines (1984-1985); Commanding Officer, 5th Battalion, 10th Marines (1992-1993); Commanding Officer, Officer Candidates School (1999-2001), Commanding General, Training Command (2002-2004), Commanding General, Training and Education Command (2006-2007). Commanding General, Marine Corps Combat Development Command (2008-2011).

Lieutenant General Flynn's staff assignments include: Forward Observer, Fire Direction Officer, Battery Executive Officer and S-4 A, 2nd Battalion, 11th Marines (1976-1979); Officer Selection Officer, Manchester, New Hampshire, (1981-1984), Operations Officer, 5th Battalion, 10th Marines (1985-1986), Plans Officer, Plans Policies and Operations Department, Headquarters Marine Corps (1987-1989); Junior Aide-de-Camp to the Commandant of the Marine Corps (1989-1991); Assistant Fire Support Coordinator, 2d Marine Division (1991-1992); Future Operations Officer, III Marine Expeditionary Force (1994-1995); Military Assistant to the Executive Secretary to the Secretary of Defense (1995-1997); Military Fellow, Council on Foreign Relations (1997-1998); Head, Strategic Initiatives Group, Headquarters Marine Corps (1998-1999); Military Secretary to the Commandant of the Marine Corps (2001-2002); Deputy Commanding General, Training and Education Command (2002-2004). Chief of Staff and Director, Command Support Center, United States Special Operations Command (2004-2006). Deputy Commanding General Multi-National Corps-Iraq (2008), Director for Joint Force Development, The Joint Staff J-7 (2011-).