Cohen is a graduate of the Maimonides School. He received his B.A. in government at Harvard University in 1977. He went on to receive a Ph.D. from Harvard in 1982 in political science, and during his PhD training went through the Army ROTC program at Massachusetts Institute of Technology.

He was an assistant professor of government and assistant dean at Harvard University from 1982 to 1985. Following this, he taught for four years at the Naval War College in the Department of Strategy, before a brief period in 1990 serving on the policy planning staff of the Office of the United States Secretary of Defense. In 1990, Cohen began his position at SAIS. Following the 1991 Persian Gulf War, he directed the U.S. Air Force's official four-volume survey, the Gulf War Air Power Survey, until 1993, for which he received the Air Force’s Exemplary Civilian Service Award. This analysis of the effect of U.S. air power was widely referenced in regards to the Revolution in Military Affairs concept.

In 1993, Paul Wolfowitz, who would later become prominent as the Deputy Secretary of Defense in the run-up to the Iraq war, became Dean of SAIS. During his brief stint at the defense policy planning staff, Cohen had worked under Wolfowitz but this was the first time they were in extended contact. In 1997, Cohen became a founding member of the Project for the New American Century, which became known as a center for prominent neoconservatives. He has been a member of the Defense Policy Board Advisory Committee, a committee of civilians and retired military officers that the U.S. Secretary of Defense may call upon for advice, since the beginning of the administration of President George W. Bush. He was put on the board after acquaintance Richard Perle put forward his name. Cohen has referred to the War on Terrorism as “World War IV”.In the run-up to the 2003 Invasion of Iraq, he was a member of Committee for the Liberation of Iraq, a group of prominent persons who pressed for an invasion.

On March 2, 2007, Cohen was appointed by Secretary of State Condoleezza Rice to serve as Counselor of the State Department, replacing Philip D. Zelikow.

Statements on US foreign policy

Cohen was one of the first neoconservatives to publicly advocate war against Iran and Iraq. In a November 2001 op-ed for the Wall Street Journal, Cohen identified what he called World War IV and advocated the overthrow of Iran's government as a possible next step for the Bush Administration. Cohen claimed "regime change" in Iran could be accomplished with a focus on "pro-Western and anticlerical forces" in the Middle East and suggested that such an action would be "wise, moral and unpopular (among some of our allies)". He went on to argue that such a policy was as important as the then identified goal of Osama Bin Laden's capture: "The overthrow of the first theocratic revolutionary Muslim state and its replacement by a moderate or secular government, however, would be no less important a victory in this war than the annihilation of bin Laden."

Later in 2001, Cohen, in what was becoming a dominant theme of his writing, advocated war against Iraq once again and proceeded to outline how effortless such a military campaign would be:

After Afghanistan, what? Iraq is the big prize... One important element will be the use of the Iraqi National Congress to help foster the collapse of the regime, and to provide a replacement for it. The INC, which has received bad, and in some cases malicious treatment, from the State Department and intelligence community over the years, may not be able to do the job with U.S. air support alone.

As a result of his public statements on why a war against Iraq was necessary, Cohen was invited to appear on CNN Wolf Blitzer Reports and amongst other statements given in response to questioning from Blitzer offered the judgement:

We know that he [Saddam Hussein] supports terror. There's very solid evidence that the Iraqis were behind an attempt to assassinate President Bush's father. And we -- by the way, we do know that there is a connection with the 9/11 terrorists. We do know that Mohamed Atta, the ringleader of the 9/11 terrorists, met with Iraqi intelligence in Prague. So...

In testifying to a Congressional House committee later in 2002 Cohen was quoted as saying:

..the choice before the United States is a stark one, either to acquiesce in a situation which permits the regime of Saddam Hussein to restore his economy, acquire weapons of mass destruction and pose a lethal threat to his neighbors and to us, or to take action to overthrow him. In my view, the latter course, with all of its risks, is the correct one. Indeed, the dangers of failing to act in the near future are unacceptable.

In a piece for the Wall Street Journal, 6 February 2003 Cohen fervently praised the presentation given by then Secretary of State Colin Powell in which he outlined the case for military action against Iraq to the United Nations. He went on to indicate that it was time for those who doubted that the case had been proven to support the Bush administration in their efforts.

An article written for the Washington Post on 10 July 2005, raised the attention of commentators in the media and "blogosphere". The piece, an attempt to articulate Cohen's self identified roles as academic, pundit, and father, was written as his son prepared to deploy to Iraq to fight a war the elder Cohen had been calling for since early 2001. The piece ends:

There is a lot of talk these days about shaky public support for the war. That is not really the issue. Nor should cheerleading, as opposed to truth-telling, be our leaders' chief concern. If we fail in Iraq -- and I don't think we will -- it won't be because the American people lack heart, but because leaders and institutions have failed. Rather than fretting about support at home, let them show themselves dedicated to waging and winning a strange kind of war and describing it as it is, candidly and in detail. Then the American people will give them all the support they need. The scholar in me is not surprised when our leaders blunder, although the pundit in me is dismayed when they do. What the father in me expects from our leaders is, simply, the truth -- an end to happy talk and denials of error, and a seriousness equal to that of the men and women our country sends into the fight.

This piece was extensively discussed in the blogosphere at the time, with some progressive blogs decrying that Cohen continued to maintain that the invasion was justified. Other commentators expressed surprise that a figure with such access and impeccable neoconservative credentials could appear to criticise the Bush Administration in such a way. Cohen later stated that he had received overwhelmingly positive responses from senior military officials in a resulting interview on C-SPAN. Cohen also continued his criticism of the conduct of the war stating that, "Those three guys [ Tommy Franks, George Tenet, and L. Paul Bremer] got the Presidential Medal of Freedom. That's just wrong."

As a member of the Defense Policy Board Advisory Committee Cohen had also been engaged in meetings involving US President George Bush. During these meetings Cohen provided advice on strategy in the Iraq conflict.

Appointment to Department of State

On 2 March 2007, it was reported by the Washington Post that Cohen was to be appointed as Condoleezza Rice's "counselor" at the United States Department of State. Cohen replaced Philip D. Zelikow and said he would fill time before appointment in April 2007 by acting as a consultant for Rice.

The tone of the Washington Post article, Cohen is described as a "critic" of the Iraq war, was soon criticised. An article by Ximena Ortiz in the National Interest Online called Cohen's ability to do the job into question and attempted to juxtapose his previous statements on the Bush administration foreign policy with the resulting war in Iraq. Adding to the criticism was Glenn Greenwald of Salon.com who, describing Cohen as "extremist a neoconservative and warmonger as it gets", suggested an internal significance of the appointment for the Bush administration:

The Cohen appointment, is clearly another instance where neoconservatives place a watchdog in potential trouble spots in the government to ensure that diplomats do not stray by trying to facilitate rapproachments between the U.S. and the countries on the neoconservative War hit list.

As the controversy was played out in the media a rebuttal of sorts from Ruth Wedgwood, international law scholar at Johns Hopkins University, sought to defend Cohen from criticism. Ortiz was subsequently supported in her criticism by fellow commentator at National Interest Online, Anatol Lieven, who raised the levels of criticism to include Cohens efforts as a historian and analyst as well as tackling other pronouncements on US foreign policy in the middle east made by Cohen.

Mearsheimer and Walt Paper

In March 2006, Harvard's Kennedy School of Government Academic Dean Stephen M. Walt along with Professor John J. Mearsheimer of the University of Chicago, both political scientists, published an academic paper titled The Israel Lobby and U.S. Foreign Policy. The paper criticizes the Israel lobby for influencing U.S. foreign policy in the Middle East away from U.S. interests and towards Israel's interests. Eliot Cohen, who is Jewish, wrote in a prominent op-ed piece in The Washington Post that the academic working paper bears all the traditional hallmarks of anti-Semitism: "obsessive and irrationally hostile beliefs about Jews", accusations toward Jews of "disloyalty, subversion or treachery, of having occult powers and of participating in secret combinations that manipulate institutions and governments", as well as selection of "everything unfair, ugly or wrong about Jews as individuals or a group" and equally systematical suppression of "any exculpatory information". Mearsheimer and Walt repeatedly denied the assertion that their paper was Anti-Semitic noting that criticism of Israeli state policy and influential American advocates of that policy, such as Cohen, is not the same thing as demonization of Jewish people.