Scheer was born to immigrant parents. His mother, a Russian Jew, and his father, a German, both worked in the garment industry. After graduating from City College of New York with a degree in economics, he studied as a fellow at the Maxwell School of Syracuse University, and then did further economics graduate work at the Center for Chinese Studies at UC Berkeley. Scheer has also been a Poynter fellow at Yale University, and was a fellow in arms control at Stanford, the same post once held by Secretary of State Condoleezza Rice.

While working at City Lights Books in San Francisco, Scheer co-authored the book, Cuba, an American tragedy (1964), with Maurice Zeitlin. Between 1964 and 1969, he served, variously, as the Vietnam correspondent, managing editor and editor-in-chief of Ramparts magazine. He reported from Cambodia, China, North Korea, Russia, Latin America and the Middle East (including the Six-Day War), as well as on national security matters in the United States. While in Cuba, where he interviewed Fidel Castro, Scheer obtained an introduction by the Cuban leader for the diary of Che Guevara ... which Scheer had already obtained, with the assistance of French journalist Michele Ray, for publication in Ramparts and by Bantam Books.

During this period Scheer made a bid for elective office as one of the first anti-Vietnam War candidates. He challenged U.S. Representative Jeffrey Cohelan in the 1966 Democratic primary. Cohelan was a liberal, but like most Democratic officeholders at that time, he supported the Vietnam War. Scheer lost, but won over 45% of the vote (and carried Berkeley), a strong showing against an incumbent that demonstrated the rising strength of New Left Sixties radicalism.

In July 1970, Scheer accompanied as a journalist a Black Panther Party delegation, led by Eldridge Cleaver, to North Korea, China, and Vietnam. The delegation also contained people from the San Francisco Red Guard, the women's liberation movement, the Peace and Freedom Party, Newsreel, and the Movement for a Democratic Military. The purpose of the delegation was to "express solidarity with the struggles of the Koreans" and to "bring back to Babylon information about their communist society and their fight against U.S. imperialism," according to the Black Panthers' publication.

After several years freelancing for magazines, including New Times and Playboy, Scheer joined the Los Angeles Times in 1976 as a reporter. There he met Narda Zacchino, a reporter whom he later wed in the paper's news room. As a national correspondent for 17 years at the Times, he wrote articles and series on such diverse topics as the Soviet Union during glasnost, the Jews of Los Angeles, arms control, urban crises, national politics and the military, as well as covering several presidential elections. The Times entered Scheer's work for the Pulitzer Prize 11 times, and he was a finalist for the Pulitzer national reporting award for a series on the television industry.

After Scheer left the Times in 1993, the paper granted him a weekly op-ed column which ran every Tuesday for the next 12 years until it was canceled in 2005. The column now appears in the San Francisco Chronicle and is distributed nationally by Creators Syndicate. He is also a contributing editor for the Nation magazine.

Scheer can be heard weekly on the nationally syndicated political analysis radio program "Left, Right & Center" produced at and syndicated by public radio station KCRW in Santa Monica.

Scheer has interviewed every president from Richard Nixon through Bill Clinton. He conducted the noted 1976 Playboy interview with Jimmy Carter, in which the then-presidential candidate admitted to having "lusted" in his heart. In an interview with George H.W. Bush, the future president and then presidential candidate revealed that he believed nuclear war was "winnable." Scheer has profiled politicians from Californians Jerry Brown and Willie Brown to Washington insiders like Henry Kissinger and Zbigniew Brzezinski, as well as entertainment figures like actor Tom Cruise.

Scheer's latest book, "The Great American Stickup: How Reagan Republicans and Clinton Democrats Enriched Wall Street While Mugging Main Street" (Nation Books), was released on September 7, 2010. Publishers Weekly wrote that the book "proves that, when it comes to the ruling sway of money power, Democrats and Republicans, Wall Street and Washington make very agreeable bedfellows.”

Scheer has written eight other books, including a collection entitled Thinking Tuna Fish, Talking Death: Essays on the Pornography of Power, With Enough Shovels: Reagan, Bush and Nuclear War, and America After Nixon: The Age of Multinationals. In 2004, Scheer published The Five Biggest Lies Bush Told Us About Iraq and made it to the Los Angeles Times Bestseller List. It was co-authored by his oldest son, Christopher Scheer, and Lakshmi Chaudhry, senior editor at Alternet.

In 2006 Scheer published Playing President: My Close Encounters with Nixon, Carter, Bush I, Reagan and Clinton — and How They Did Not Prepare Me for George W. Bush; in 2008 he published The Pornography of Power: How Defense Hawks Hijacked 9/11 and Weakened America.

Scheer has taught courses at Antioch College, City College of New York, UC Irvine, UCLA and UC Berkeley. He is now a senior lecturer at the University of Southern California's Annenberg School for Communication, where he teaches two courses each semester on media and society.

Scheer was the 1998 honoree of the Shelter Partnership, an organization of Los Angeles downtown businesses, and the USC School of Social Work's Los Amigos award recipient. He won the James Aronson Award for Social Justice Journalism for his writing in the Los Angeles Times and The Nation about the case of nuclear scientist Wen Ho Lee. He has also received awards and citations from Stanford University, the Moscow Academy of Sciences, the University of California, San Diego, and Yale University.

Scheer and his son were creative script consultants on the Oliver Stone film, Nixon, which was nominated for an Academy Award for best original screenplay. He has appeared in small speaking roles as a journalist in several feature films, including The Siege and Bulworth. In 2005, the Mill Valley Film Festival premiered a documentary on the activist and philanthropist Stanley Sheinbaum which Scheer co-produced.

Iraq War

In an August 6, 2002, article, he wrote that "a consensus of experts" informed the Senate that the Iraqi weapons arsenal was “almost totally destroyed during eight years of inspections.” On June 3, 2003, Scheer concluded that White House justifications for the war were a "big lie." On November 4, 2003, he penned an article in favor of withdrawal from Iraq.

World War II

In an April 7, 2010, article he wrote that Harry Truman perpetrated "the most atrocious act of terrorism in world history when he annihilated the civilian populations of Hiroshima and Nagasaki." Scheer repeated these allegations on the radio program "Left, Right and Center".

Support of Republican Candidate for Kentucky Senate

In the October 1, 2010, episode of the radio show "Left, Right and Center", Scheer, a self-described Liberal, expressed support for Rand Paul, son of former Libertarian presidential candidate Ron Paul, in his bid for the 2011-2016 Kentucky Senate seat.

Scheer has often expressed highly controversial thoughts. For example, on February 15, 2005, Scheer wrote an article entitled " What We Don't Know About 9/11 Hurts Us" for the LA Times. In it, he asked, "Would George W. Bush have been reelected president if the public understood how much responsibility his administration bears for allowing the 9/11 attacks to succeed?" After running his column for more than 12 years and working as a reporter for the paper 17 years prior, the Los Angeles Times ended a nearly thirty year relationship with Scheer in November 2005, citing the need to cut costs while subsequently replacing him with two right-wing columnists. Scheer said in an interview with "Democracy Now!" that the paper's owner, the Tribune Company, currently owns a newspaper and a television station in the same market, which is illegal Newspaper/ Broadcast Cross-Ownership — FCC News The FCC’s newspaper-broadcast cross-ownership rule: an analysis — Economic Policy Institute, and may have fired Scheer in an attempt to make it easier to obtain a waiver permitting the dual ownership from the Federal Communications Commission (FCC). He also commented during a November 14, 2005, appearance on Democracy Now! that,

"What happened is that I had been the subject of vicious attacks by Bill O'Reilly and Rush Limbaugh. I was a punching bag for those guys. I'm still standing, and the people who run the paper collapsed."

In a posting at the Huffington Post, Scheer wrote:

"The publisher Jeff Johnson, who has offered not a word of explanation to me, has privately told people that he hated every word that I wrote. I assume that mostly refers to my exposing the lies used by President Bush to justify the invasion of Iraq. Fortunately 60 percent of Americans now get the point but only after tens of thousand of Americans and Iraqis have been killed and maimed as the carnage spirals out of control. My only regret is that my pen was not sharper and my words tougher."

Scheer's firing incited a protest held outside the Times downtown office on November 15, and hundreds of readers wrote letters of complaint while some, including actress Barbra Streisand, publicly announced the cancellation of their Times subscriptions. Within a few days of his column being retired by the Times, the San Francisco Chronicle offered itself as the new home paper of Scheer's syndicated column, which now runs on Wednesdays there and elsewhere. On November 29, 2005, he co-launched, as editor in chief, a new online magazine called Truthdig. In 2007, Truthdig was a finalist for three Webby Awards, in the news, blog (political), and politics categories; the site won both the People's Voice and professional jury prizes in the Political Blog category. In 2010, Truthdig again received the Webby Award jury prize for best political blog.