She then joined the Institute for National Strategic Studies at the National Defense University as a distinguished research professor, founding and leading NDU's Quadrennial Defense Review working group, which had been chartered by the Chairman of the Joint Chiefs of Staff to develop intellectual capital in preparation for the Defense Department’s upcoming QDR in 2001. She then moved to the Center for Strategic and International Studies, where she was a Senior Advisor working on a range of defense policy and international security issues before co-founding the Center for a New American Security, to which she was named President, in 2007 with Kurt M. Campbell. Flournoy and CNAS co-founder Kurt Campbell wrote a policy paper called "The Inheritance and the Way Forward" that advocated for a U.S. foreign policy "grounded in a common-sense pragmatism rather than ideology".
Obama administration
After the 2008 presidential election, she was selected as one of the Review Team Leads for the Obama transition at the Department of Defense. On January 8, 2009, President-elect Obama announced that he was nominating her as Under Secretary of Defense for Policy, to serve under Secretary of Defense Robert Gates. In his memoirs, Secretary Gates wrote that he had "developed high respect for" Flournoy, whom he characterized as "clear-thinking and strong". On December 12, 2011, Flournoy announced that she would step down in February 2012 to return to private life and contribute to President Barack Obama's re-election bid. As part of the Obama campaign, Flournoy appeared in a message from the official Democrat Twitter feed on October 22, 2012. She was shown in a video responding to GOP candidate Mitt Romney's assertion that Russia was the US's "number-one geopolitical foe" by stating Romney's was "a really curious statement, given that the Cold War has been over for some time."
Affiliations
In 2017, Flournoy co-founded WestExec Advisors, a strategic advisory firm that advises U.S. and international companies and financial institutions on geopolitical factors that affect their business strategy and investment portfolios. She previously served as a Senior Advisor to the Boston Consulting Group's Washington D.C.-based public sector practice. She is a Senior Fellow at Harvard's Belfer Center for Science and International Affairs. She also serves on the Board of Directors of the Center for a New American Security, the Atlantic Council, and Women in International Security. She is a member of the Aspen Strategy Group, the Council on Foreign Relations, and the CIA's External Advisory Board. She is a former member of the guiding coalition of the Project on National Security Reform, the Defense Policy Board, and the Defense Science Board Task Force on Transformation. Flournoy is an Advisory Board Member of Spirit of America, a 501 organization that supports the safety and success of Americans serving abroad and the local people and partners they seek to help.