Currently a principal in the Scowcroft Group, Jim Pavitt was Deputy Director of Operations for the Central Intelligence Agency from 1999 to 2004, succeeding Jack Downing in heading the U.S. civilian covert action and human-source intelligence programs, and himself being succeeded by Steve Kappes. He was criticized for underestimating the threat of al-Qaeda by CIA Inspector General John Helgerson, along with George Tenet and Cofer Black. Helgerson recommended censure to then Director Porter Goss.
He was a career employee, who entered as a trainee after duty as an Army intelligence officer and working as a legislative assistant. Pavitt had a number of overseas postings. 
In 1990, he was detailed to the National Security Council as Director of Intelligence Programs where he provided the President and other senior policymakers with analysis and advice on critical intelligence related issues. He became Senior Director and Special Assistant to the President for Intelligence Programs in 1992.
Following his return from the National Security Council, he had a number of assignments related to counterproliferation, including Deputy Director of the DCI Nonproliferation Center, which is now known as the DCI Weapons Intelligence, Nonproliferation, and Arms Control Center. Before that, he served as Chief of the Counterproliferation Division in the Directorate of Operations. He became Associate Deputy Director for Operations in July 1997.
Richard Clarke said Pavitt opposed a number of proposed attempts to capture or kill Osama bin Laden, and blocked CIA use of armed MQ-1 Predator drones against terrorists.  Michael Scheuer also criticized his leadership. 
- CIA Deputy Director for Operations Announces Retirement, Central Intelligence Agency, June 4, 2004
- "CIA 9/11 review recommends disciplinary proceedings", USA Today, 26 August 2005
- DCI Announces Departure of Jack Downing; DCI Tenet Announces Departure of Deputy Director for Operations, Names Successor, Central Intelligence Agency, May 7, 1999
- Steve Coll (2004), Ghost Wars: the Secret History of the CIA, Afghanistan and bin Laden, from the Soviet Invasion to September 10, 2001, Penguin,p. 540
- Richard A. Clarke (2004), Against all Enemies: Inside America's War on Terror, Free Press, Simon & Schuster, ISBN 0743260244, p. 205
- Clarke, p. 211
- Rebecca Leung (November 14, 2004), "Bin Laden Expert Steps Forward", 60 Minutes, CBS News