Work in academia

Pipes returned to Harvard in 1973 and, after further studies abroad (in Freiburg-im-Breisgau and Cairo), obtained a Ph.D. in medieval Islamic history in 1978. His Ph.D. dissertation eventually became his first book, Slave Soldiers and Islam, in 1981. He switched his academic interest from medieval Islamic studies to modern Islam in the late 1970s, with the rise of Ayatollah Khomeini and the Iranian revolution.

He taught world history at the University of Chicago from 1978 to 1982, history at Harvard from 1983 to 1984, and policy and strategy at the Naval War College from 1984 to 1986. In 1982-83, Pipes served on the policy-planning staff at the State Department in 1982–83.

Post-academia

Pipes largely left academia after 1986, although he taught a course titled "International Relations: Islam and Politics" as a visiting professor at Pepperdine University's School of Public Policy in 2007. Pipes told an interviewer from Harvard Magazine that he has "the simple politics of a truck driver, not the complex ones of an academic. My viewpoint is not congenial with institutions of higher learning."

From 1986 on, Pipes worked for various think tanks. From 1986 to 1993 he was director of the Philadelphia-based Foreign Policy Research Institute (FPRI) and editor of its journal, Orbis. In 1990 he organized the Middle East Forum as a unit of FPRI; it became an independent organization with himself as head in January 1994. Pipes edited its journal, the Middle East Quarterly, until 2001. He established Campus Watch as a project of the Middle East Forum in 2002, followed by the Legal Project in 2005, Islamist Watch in 2006, and the Washington Project in 2009.

In 2003, President George W. Bush nominated Pipes for the board of the United States Institute of Peace. A filibuster was launched by Democratic Senators in the United States Senate against Pipes' nomination. Senator Tom Harkin said that he was "offended" by Pipes' comments on Islam, and that while "some people call [Pipes] a scholar... this is not the kind of person you want on the USIP." While defending Pipes' nomination, White House spokesman Ari Fleischer distanced Bush from Pipes's views, saying that Bush "disagrees with Pipes about whether Islam is a peaceful religion". Pipes obtained the position by recess appointment and served on the board until early 2005. His nomination was protested by Muslim groups in the U.S., and Democratic leaders, who cited his oft-stated belief that victory is the most effective way to terminate conflict. The Los Angeles Times wrote that "in trying to prevent Middle East scholar Daniel Pipes from joining the board of the U.S. Institute of Peace, Sens. Edward M. Kennedy (D-Mass.), Christopher J. Dodd (D-Conn.) and Tom Harkin (D-Iowa) are abusing their privilege."