Thomas Emmet Hayden was born in Royal Oak, Michigan, to parents of Irish ancestry, Genevieve Isabelle (née Garity) and John Francis Hayden. His father was a former Marine who worked for Chrysler as an accountant and was also a violent drunk. When Hayden was ten, his parents divorced and his mother raised him. A smart kid, Hayden attended a Catholic elementary school, where he read out loud to nuns and "learned to fear hell," and later graduated from Dondero High School in Royal Oak, Michigan, class of 1956. While at Dondero High School, Hayden edited the school paper and after using the first letter of successive paragraphs to spell "Go to hell" in his farewell column, he was banned from attending his graduation ceremony and only received a diploma. Hayden grew up attending a church led by Charles Coughlin, a Catholic priest noted for his anti-Semite teachings and who was also known nationally during the time of The Great Depression as the "radio priest." Hayden's dismay with Coughlin caused him to break with the Catholic Church as a teenager.

Writing about Hayden's role in the 1960s New Left, Nicholas Lemann, national correspondent for The Atlantic, said that "Tom Hayden changed America", calling him "father to the largest mass protests in American history", and Richard N. Goodwin, who was a speechwriter for Presidents Lyndon B. Johnson and John F. Kennedy, said that Hayden, "without even knowing it, inspired the Great Society. Staughton Lynd, though, was critical of the Port Huron and New Left concept of "participatory democracy" stating, "we must recognize that when an organization grows to a certain size, consensus decision-making is no longer possible and some form of representative government becomes necessary."

He later attended the University of Michigan, where he was Editor of the Michigan Daily and, disenchanted by the anti-radicalism of existing groups like the National Student Association, was one of the initiators of the influential leftist student Activist group Students for a Democratic Society (SDS). In 1961, Hayden married Sandra "Casey" Cason, a civil rights Activist who worked for the Student Nonviolent Coordinating Committee (SNCC). Hayden became a "freedom rider" in the South and then served as President of SDS from 1962 to 1963.

From 1964 to 1968, Hayden lived in Newark, New Jersey, where he worked with impoverished inner-city residents as part of the Newark Community Union Project. He was also witness to the city's race riots of 1967, driven by far more than race alone, as Hayden would point out; and wrote the book Rebellion in Newark: Official Violence and Ghetto Response (1967).

In 1965, Hayden, along with Communist Party USA member Herbert Aptheker and Quaker peace Activist Staughton Lynd undertook a controversial visit to North Vietnam and Hanoi. The three toured villages and factories and met with an American POW whose plane had been shot down. The result of this tour of North Vietnam, at a high point in the war, was a book titled The Other Side. Staughton Lynd later wrote that the New Left disavowed "the Anti-Communism of the previous generation" and that Lynd and Hayden had written, in Studies on the Left, "We refuse to be anti-Communist, We insist the term has lost all the specific content it once had."

In 1968, Hayden played a major role in the protests outside the Democratic National Convention in Chicago, Illinois, broken up by what was later called by the U.S. National Commission on the Causes and Prevention of Violence "a police riot". Six months after the convention he and seven other protesters including Abbie Hoffman and Jerry Rubin were indicted on federal charges of conspiracy and incitement to riot as part of the "Chicago Eight", a.k.a. the "Chicago Seven" after Bobby Seale's case was separated from the others. Hayden and four others were convicted of crossing state lines to incite a riot, but the charges were later reversed and remanded on appeal. The government did not retry the case and thereafter elected to dismiss the substantive charges. United States v. Dellinger, 472 F.2d 340 (7th Cir. 1972), cert. denied, 410 U.S. 970, 93 S.Ct. 1443, 35 L.Ed.2d 706 (1973).

Hayden also founded the Indochina Peace Campaign (IPC), which operated from 1972 to 1975. The IPC, operating in Boston, New York, Detroit and Santa Clara, mobilized dissent against the Vietnam War, demanded unconditional amnesty for U.S. draft evaders, among other aims. Jane Fonda, a supporter of the IPC, later turned this moniker into a name for her film production firm, IPC Films, which produced in whole or in part, movies and documentaries such as F.T.A. (1972), Introduction to the Enemy (1974), The China Syndrome (1979), Nine to Five (1980) and On Golden Pond (1981). Hayden and Fonda divorced in 1990.

Hayden made several subsequent well-publicized visits to North Vietnam as well as Cambodia during America's involvement in the 'Vietnam War' which had expanded under President Richard M. Nixon to include the adjoining nations of Laos and Cambodia, although he did not accompany his Future wife, Actress Jane Fonda, on her especially controversial trip to Hanoi in the spring of 1972. The next year he married Fonda and they had one child, Troy Garity, born on 7 July 1973. In 1974, while the Vietnam War was still ongoing, the documentary film Introduction to the Enemy was released, a collaboration by Fonda, Hayden, Haskell Wexler and others. It depicts their travels through North and South Vietnam in spring 1974.

During 1976, Hayden made a primary-election challenge to then serving California U.S. Senator John V. Tunney. "The radicalism of the 1960s is fast becoming the Common sense of the 1970s," the New York Times reported him saying at the time. Starting far behind, Hayden mounted a spirited campaign and finished a surprisingly close second in the Democratic primary. He and Fonda later initiated the Campaign for Economic Democracy (CED), which formed a close alliance with then-Governor Jerry Brown and promoted solar Energy, environmental protection and renters' rights policies, as well as candidates for local office throughout California, more than 50 of whom would go on to be elected.

Hayden later served in the California State Assembly (1982–1992) and the State Senate (1992–2000). During this time, he was frequently protested by conservative groups, including Vietnamese refugees, veterans of the U.S. military and Young Americans for Freedom. He mounted a bid in the Democratic primary for California Governor during 1994 on the theme of campaign Finance reform, and ran for Mayor of Los Angeles during 1997, losing to incumbent Republican Richard Riordan.

During 1999, Hayden made a speech for the Seattle WTO protests. During 2001, he unsuccessfully sought election to the Los Angeles City Council. Hayden served as a member of the advisory board for the Progressive Democrats of America, an organization created to increase progressive political cooperation and influence within the Democratic Party. He served on the advisory board of the Levantine Cultural Center, a nonprofit organization founded in Los Angeles in 2001 that champions cultural literacy about the Middle East and North Africa. During January 2008, Hayden wrote an opinion essay for the Web site The Huffington Post endorsing Barack Obama's presidential bid in the Democratic primaries. In that same year, he helped initiate Progressives for Obama (now called Progressive America Rising), a group of political progressives that provided assistance for Obama in his initial presidential campaign.

During 2007, Akashic Books released Hayden's Ending the War in Iraq. In a discussion about the book with Theodore Hamm, published in the Brooklyn Rail, Hayden argues: "The apparatus of occupation is never going to turn into a peacekeeping economic development agency. We need to withdraw our stamp of approval and our tax dollars from supporting the occupation. That doesn't mean that there can't be some attempts at remedies but there should never be used as an excuse to stay."

Hayden lived in Los Angeles and was married to his third wife, Barbara Williams, at the time of his death. He and Williams adopted a son, Liam (born 2000). Hayden died in Santa Monica, California on October 23, 2016, aged 76, following a lengthy illness, including a stroke.

Hayden taught numerous courses on social movements, two at Scripps College — one on the Long War and one on gangs in America — and a course called "From the '60s to the Obama Generation" at Pitzer College. He also taught at Occidental College and at Harvard University's Institute of Politics. He taught a class at University of California, Los Angeles on protests from Port Huron to the present. Hayden taught a class in Political Science at the University of Southern California during the 1977-78 school year. He was the author or Editor of 19 books, including The Long Sixties: From 1960 to Barack Obama, Writings for a Democratic Society: The Tom Hayden Reader, and his memoir, Reunion, and served on the editorial board of The Nation. His book Hell No: The Forgotten Power of the Vietnam Peace Movement, completed in the months before his death in October 2016, was published on January 31, 2017, by Yale University Press.