Seventh United States Army/United States Army Europe, 2005–2008
International Security Assistance Force and United States Forces – Afghanistan, 2008–2009
McKiernan gained experience in the Balkans as a staff officer in the 1990s. In July 1996, McKiernan joined the Allied Rapid Reaction Corps, serving as the Deputy Chief of Staff G2/G3, forward deployed in both Sarajevo, Bosnia-Herzegovina and Rheindahlen, Germany. From August 1998 until September 1999, he served as Deputy Chief of Staff, Operations, Headquarters, United States Army, Europe and Seventh Army during a period of simultaneous operations in Bosnia, Albania, and Kosovo. Prior to these appointments McKiernan served in the VII Corps Headquarters during the Gulf War and then as the G3 in the 1st Cavalry Division in the rank of lieutenant colonel. The first appointment was probably his first experience of working with other officers or formed units of other nationalities, in the second he had British Exchange Officers on his staff. In 2001, McKiernan was assigned as G3, Headquarters, Department of the Army. Following that posting, in September 2002, General McKiernan assumed command of the Third United States Army and United States Army Forces Central Command, and became the Coalition Forces Land Component Commander for United States Central Command in preparation for Operation Iraqi Freedom. In March 2003, McKiernan led all coalition and United States conventional ground forces that attacked Iraq to remove Saddam Hussein from power. Following his assignment as ground forces commander, McKiernan was assigned as Deputy Commanding General/Chief of Staff for United States Army Forces Command, the largest major command in the Army which is responsible for the readiness and deployment of army forces based in the United States. Then he assumed command of Seventh Army/United States Army Europe. He was then assigned to Afghanistan as Commander, International Security Assistance Force and United States Forces-Afghanistan from June 3, 2008, to June 15, 2009.
In their book, Cobra II, military historians Michael Gordon and Bernard E. Trainor suggest that McKiernan was unhappy to hear of the cancellation of the deployment of the 1st Cavalry Division, a 17,000-soldier force that was scheduled to arrive in Iraq as a follow-on reinforcement. Its deployment was cancelled on April 21, 2003, after U.S. Defense Secretary Donald Rumsfeld raised the issue of whether it was needed. Previously, shortly before the war, McKiernan won Pentagon approval for a new war plan that increased the number of ground troops, calling the new war plan COBRA II. During Operation Iraqi Freedom, McKiernan had a different view of the battlefield than his superior, General Tommy Franks. McKiernan saw the Fedayeen Saddam fighters as a major threat and one of the "centers of gravity" in Iraq, while Franks dismissed the importance of the irregulars. The military was also surprised when McKiernan and his staff were not given command for post-war operations in Iraq, which instead went to V Corps and the newly promoted Lieutenant General Ricardo Sanchez.
Targeted killing
In a 2008 interview by Der Spiegel, McKiernan was asked whether Germany was a particularly difficult ally considering that its government requested limitations on its soldiers' deployment in Afghanistan, feeling that it might violate Germany's constitution if they were to conduct a targeted killing in the absence of a direct attack. McKiernan responded:
