He joined the United States Department of Justice Antitrust Division in 1992, working there until 1993.

In 1993-94, he returned to the State Department and headed an interagency team representing the United States at an international arbitration relating to the U.S.'s longstanding dispute with the United Kingdom related to U.S. airlines' access to London Heathrow Airport.

In 2001, Witten was promoted to Deputy Legal Adviser of the Department of State, serving under Legal Adviser William Howard Taft IV, and, after Taft's departure in 2005, John B. Bellinger III.

He was one of four State Department Deputy Legal Advisers, the top-ranking position for a career lawyer at the State Department, and supervised legal matters including international law enforcement cooperation, human rights and refugees, and international economic issues.

In June 2007, Witten was appointed Principal Deputy Assistant Secretary of State for Population, Refugees, and Migration.