Pavitt joined the CIA in 1973 as a Career Trainee with postings to Europe, Asia and Washington. He was posted to Vienna (1976-1978), East Berlin (1978-1980), Budapest, Hungary and Malaysia (1980-1983). He was expelled (PNG'd) from East Germany. He was chief of station in Luxembourg (1983-1986). He served as a Branch Chief in the Africa Division. From 1990 to 1993, he served on the National Security Council team under Brent Scowcroft as Senior Intelligence Advisor to President George H.W. Bush. After being assigned to work across the Agency operational/analytical divide in the Directorate of Intelligence, he became the founder and first Chief of the Directorate of Operation's "Counterproliferation Division" (CPD). Gordon Oehler, then Chief of the Directorate of Intelligence's Non-Proliferation Center, criticized this as being redundant and stepping on his turf. This was considered a specious critique by veteran Agency HUMINT Operations Officers, however, especially those who had been assigned under Oehler previously and realized that Oehler held HUMINT counterproliferation operations—indeed, covert operations in general—in considerable disdain. Pavitt hand picked operations officers, some of which were Nonofficial Cover Officers (NOCs) including Valerie Plame, to staff the CPD. In 1997 he was appointed Associate Deputy Director of Operations. He was Deputy Director of Operations from 1999 until his resignation in 2004. In 2003, the CPD took down the nuclear black market being operated by Abdul Qadeer Khan.