He left that post in 2001 and became the Frederick Schultz Professor at Princeton University's Woodrow Wilson School.
From 2002 to 2009 Barton was Co-Director of the Post-Conflict Reconstruction Project at the Center for Strategic and International Studies (CSIS), where he served as an expert adviser to the Iraq Study Group, led conflict-related working groups for the United States Institute of Peace and the Princeton Project on National Security, and produced reports on Iraq, Afghanistan, Sudan, Pakistan, religion in conflict, measurement of progress, and U.S. legislative policy.