After John Lennon's death, historian Jon Wiener filed a Freedom of Information Act request for FBI files on Lennon, which document the Bureau's role in the Nixon Administration attempt to deport Lennon in 1972 to stop his anti-war campaign before the Nixon re-election campaign. The FBI admitted it had 281 pages in its files on Lennon but refused to release most of them, they contained "national security" information. In 1983, Wiener sued the FBI with the help of the American Civil Liberties Union of Southern California, it took fourteen years of litigation to force the FBI to release the withheld pages. The ACLU, representing Wiener, won a favorable decision in their suit against the FBI in the Ninth Circuit in 1991. The Justice Department appealed the decision to the Supreme Court in April, 1992, but the court declined to review the case. The Justice Department settled most of the outstanding issues in the case outside the court in 1997, when all but 10 of the contested documents were released,, respecting President Bill Clinton's new rule that documents should be withheld only if releasing them would involve "foreseeable harm." In January 2000, he published a book titled Gimme Some Truth, The John Lennon FBI Files, referring to the same titled song of Lennon, from the University of California Press which contains facsimiles of the documents, including "lengthy reports by confidential informants detailing the daily lives of anti-war activists, memos to the White House, transcripts of TV shows on which Lennon appeared, and a proposal that Lennon be arrested by local police on drug charges". The story is told in the documentary The U.S. Versus John Lennon, by David Leaf and John Scheinfeld, released in theaters in September 2006. The final 10 documents in Lennon's FBI file, which had been withheld as containing "national security information provided by a foreign government under an explicit promise of confidentiality," and reported on Lennon's ties with London anti-war activists in 1971, were released in December 2006.

In his 2005 book Historians in Trouble (The New Press), Wiener examines cases of historians accused of misconduct.

His earlier books include Come Together: John Lennon in His Time (Random House, 1984), an account of Lennon’s place in the radical politics and counterculture of the 1960s.

Wiener started writing for The Nation in 1984 and has published more than 100 articles there. His work has also appeared in the New York Times Magazine, The New Republic, and the Los Angeles Times. His scholarly articles have appeared in The American Historical Review, The Journal of American History, and Past & Present.

Wiener hosts a weekly afternoon drive-time interview show on KPFK 90.7 FM in Los Angeles. His guests have included Gail Collins, Jane Mayer, Barbara Ehrenreich, Rick Hertzberg, Tom Frank, Pico Iyer, Michel Pollan, Seymour Hersh, Howard Zinn, Terry Gross, and Ira Glass.

Wiener is a graduate of St. Paul Central High School, has a B.A. from Princeton University, a Ph.D. from Harvard University, and has taught at UC Irvine since 1973. He lives in Los Angeles and is married to video artist and photographer Judy Fiskin.