Baez was born on Staten Island, New York, on January 9, 1941. Joan's grandfather, the Reverend Alberto Baez, left the Catholic Church to become a Methodist minister and moved to the U.S. when her Father was two years old. Her Father, Albert Baez (1912–2007), was born in Puebla, Mexico and grew up in Brooklyn, New York, where his Father preached to—and advocated for—a Spanish-speaking congregation. Albert first considered becoming a minister but instead turned to the study of mathematics and physics and received his Ph.D. degree at Stanford University in 1950. Albert was later credited as a co-inventor of the x-ray microscope. Joan's cousin, John C. Baez, is a mathematical Physicist.

In 1956, Baez first heard Martin Luther King, Jr., speak about nonviolence, civil rights and social change which brought tears to her eyes. Several years later, the two became friends, with Baez participating in many of the Civil Rights Movement demonstrations that Dr. King helped organize.

The opening line of Baez's memoir And a Voice to Sing With is "I was born gifted" (referencing her singing voice, which she explained was given to her and for which she can take no credit). A friend of Joan's Father gave her a ukulele. She learned four chords, which enabled her to play rhythm and blues, the music she was listening to at the time. Her parents, however, were fearful that the music would lead her into a life of drug addiction. When Baez was 13, her aunt and her aunt's boyfriend took her to a concert by folk musician Pete Seeger, and Baez found herself strongly moved by his music. She soon began practicing the songs of his repertoire and performing them publicly. One of her very earliest public performances was at a retreat in Saratoga, California for a youth group from Temple Beth Jacob, a Redwood City, California Jewish congregation. A few years later in 1957, Baez bought her first Gibson acoustic guitar.

In 1958, at age 17, Baez committed her first act of civil disobedience by refusing to leave her Palo Alto High School classroom in Palo Alto, California, for an air raid drill.

Her true professional career began at the 1959 Newport Folk Festival. Following that appearance, she recorded her first album for Vanguard, Joan Baez (1960), produced by Fred Hellerman of The Weavers, who produced many albums by folk artists. The collection of traditional folk ballads, blues, and laments sung to her own guitar accompaniment sold moderately well. It featured many popular Child Ballads of the day and was recorded in only four days in the ballroom of New York City's Manhattan Towers Hotel. The album also included "El Preso Numero Nueve", a song sung entirely in Spanish, which she would re-record in 1974 for inclusion on her Spanish-language album, Gracias a la Vida.

Baez's distinctive vocal style and political activism had a significant impact on popular music. She was one of the first Musicians to use her popularity as a vehicle for social protest, singing and marching for human rights and peace. Pete Seeger, Odetta, and decades-long friend Harry Belafonte were her early social justice advocate influences. Baez came to be considered the "most accomplished interpretive folksinger/songwriter of the 1960s". Her appeal extended far beyond the folk-music audience. Of her fourteen Vanguard albums, thirteen made the top 100 of Billboard's mainstream pop chart, eleven made the top forty, eight made the top twenty, and four made the top ten.

Baez first met Dylan in 1961 at Gerde's Folk City in New York City's Greenwich Village. At the time, Baez had already released her debut album and her popularity as the emerging "Queen of Folk" was on the rise. Baez was initially unimpressed with the "urban hillbilly", but was impressed with one of Dylan's first compositions, "Song to Woody" and remarked that she would like to record it.

From the early-to-mid-1960s, Baez emerged at the forefront of the American roots revival, where she introduced her audiences to the then-unknown Bob Dylan, and was emulated by artists such as Judy Collins, Emmylou Harris, Joni Mitchell, and Bonnie Raitt. On November 23, 1962, Baez appeared on the cover of Time Magazine—a rare honor then for a musician.

By 1963, Baez had already released three albums, two of which had been certified gold, and she invited Dylan on stage to perform alongside her at the Newport Folk Festival. The two performed the Dylan composition "With God on Our Side", a performance that set the stage for many more duets like it in the months and years to come. Typically while on tour, Baez would invite Dylan to sing on stage partly by himself and partly with her, much to the chagrin of her fans.

Highly visible in civil-rights marches, Baez became more vocal about her disagreement with the Vietnam War. In 1964, she publicly endorsed resisting taxes by withholding sixty percent of her 1963 income taxes. In 1964, she founded the Institute for the Study of Nonviolence (along with her mentor Sandperl) and encouraged draft resistance at her concerts. The Institute for the Study of Nonviolence would later branch into the Resource Center for Nonviolence.

By the time of Dylan's 1965 tour of the UK, their relationship had slowly begun to fizzle out after they had been romantically involved off and on for nearly two years. The tour and simultaneous disintegration of their relationship was documented in D. A. Pennebaker's documentary film Dont Look Back (1967).

In 1966, Baez's autobiography, Daybreak, was released. It is the most detailed report of her life through 1966 and outlined her anti-war position, dedicating the book to men facing imprisonment for resisting the draft.

In October 1967, Baez and her mother, along with nearly 70 other women, were arrested at the Oakland, California, Armed Forces Induction Center for blocking its doorways to prevent entrance by young inductees, and in support of young men who refused military induction. They were incarcerated in the Santa Rita Jail, and it was here that Baez met David Harris, who was kept on the men's side but who still managed to visit with Baez regularly.

After finding a pacifist preacher and a church outfitted with peace signs and writing a blend of Episcopalian and Quaker wedding vows, Baez and Harris married in New York City on March 26, 1968. Her friend Judy Collins sang at the ceremony. After the wedding, Baez and Harris moved into a home in the Los Altos Hills on 10 acres (4.0 hectares) of land called Struggle Mountain, part of a commune, where they tended gardens and were strict vegetarians.

Their son Gabriel was born on December 2, 1969. Harris was released from Texas prison after 15 months, but the relationship began to dissolve and the couple divorced amicably in 1973. They shared custody of Gabriel, who lived primarily with Baez. Explaining the split, Baez wrote in her autobiography: "I am made to live alone." Baez and Harris remained on friendly terms throughout the years; they reunited on-camera for the 2009 American Masters documentary for the USA’s PBS. Their son Gabriel is a Drummer and occasionally tours with his mother. He has a daughter Jasmine who also sang with Joan Baez at Kidztock in 2010.

Baez's experiences regarding Vietnam's human-rights violations ultimately led her to found her own human-rights group in the late 1970s, Humanitas International, whose focus was to target oppression wherever it occurred, criticizing right and left-wing régimes equally.

During this period in late 1971, she reunited with Composer Peter Schickele to record two tracks, "Rejoice in the Sun" and "Silent Running" for the science-fiction film Silent Running. The two songs were issued as a single on Decca (32890). In addition to this, another LP was released on Decca (DL 7-9188) and was later reissued by Varèse Sarabande on black (STV-81072) and green (VC-81072) vinyl. In 1998, a limited release on CD by the "Valley Forge Record Groupe" was released.

Baez wrote and composed at least three songs that were specifically about Dylan. In "To Bobby", written in 1972, she urged Dylan to return to political activism, while in "Diamonds & Rust", the title track from her 1975 album, she revisited her feelings for him in warm, yet direct terms. "Winds of the Old Days", also on the Diamonds & Rust album, is a bittersweet reminiscence about her time with "Bobby".

Where Are You Now, My Son? (1973) featured a 23-minute title song which took up all of the B-side of the album. Half spoken word poem and half tape-recorded sounds, the song documented Baez's visit to Hanoi, North Vietnam, in December 1972 during which she and her traveling companions survived the 11-day-long Christmas Bombings campaign over Hanoi and Haiphong. (See Vietnam War in Civil rights section below.)

Gracias a la Vida (1974) (the title song written and first performed by Chilean folk singer Violeta Parra) followed and was a success in both the U.S. and Latin America. It included the song "Cucurrucucú paloma". Flirting with mainstream pop music as well as writing her own songs for Diamonds & Rust (1975), the album became the highest selling of Baez's career and included a second top-ten single in the form of the title track.

Baez toured with Dylan as a performer on his Rolling Thunder Revue in 1975–76. She sang four songs with Dylan on the live album of the tour, The Bootleg Series Vol. 5: Bob Dylan Live 1975, The Rolling Thunder Revue, released in 2002. Baez appeared with Dylan in the one-hour TV special Hard Rain, filmed at Fort Collins, Colorado, in May 1976. Baez also starred as 'The Woman In White' in the film Renaldo and Clara (1978), directed by Bob Dylan and filmed during the Rolling Thunder Revue. Dylan and Baez toured together again in 1984 along with Carlos Santana.

In 1976, she was awarded the Thomas Merton Award for her ongoing activism.

Her song "Altar Boy and the Thief" from Blowin' Away (1977) was written as a dedication to her gay fanbase.

Baez has also been prominent in the struggle for gay and lesbian rights. In 1978, she performed at several benefit concerts to defeat the Briggs Initiative, which proposed banning all gay people from teaching in the public schools of California. Later that same year, she participated in memorial marches for the assassinated San Francisco city supervisor, Harvey Milk, who was openly gay.

Baez's first real boyfriend was Michael New, a young man whom she met at her college. Years later in 1979, he inspired her song "Michael". New was a fellow student from Trinidad who, like Baez, attended classes only occasionally. The two spent a considerable amount of time together, but Baez was unable to balance her blossoming career and her relationship. The two bickered and made up repeatedly, but it was apparent to Baez that New was beginning to resent her success and new-found local Celebrity. One night she saw him kissing another woman on a street corner. Despite this, the relationship remained intact for several years after the two moved to California together in 1960.

Baez dated Apple Computer cofounder Steve Jobs during the early 1980s. A number of sources have stated that Jobs—then in his mid-20s—had considered asking Baez to marry him, except that her age at the time (early 40s) made the possibility of their having children unlikely. Baez mentioned Jobs in the acknowledgments in her 1987 memoir And a Voice to Sing With and performed at the memorial for him in 2011. After Jobs' death, Baez spoke fondly about him, stating that even after the relationship had ended, the two remained friends, with Jobs having visited Baez shortly before his death, and stating that "Steve had a very sweet side, even if he was as . . . erratic as he was famous for being".

She toured Chile, Brazil and Argentina in 1981, but was prevented from performing in any of the three countries, for fear her criticism of their human-rights practices would reach mass audiences if she were given a podium. While there, she was kept under surveillance and subjected to death threats. A film of the ill-fated tour, There But for Fortune: Joan Baez in Latin America, was shown on PBS in 1982.

Baez found herself without an American label for the release of Live Europe 83 (1984), which was released in Europe and Canada but not released commercially in the U.S. She did not have an American release until the album Recently (1987) on Gold Castle Records.

Baez also played a significant role in the 1985 Live Aid concert for African famine relief, opening the U.S. segment of the show in Philadelphia, Pennsylvania. She has toured on behalf of many other causes, including Amnesty International's 1986 A Conspiracy of Hope tour and a guest spot on their subsequent Human Rights Now! tour.

In 1987, Baez's second autobiography called And a Voice to Sing With was published and became a New York Times bestseller. That same year, she traveled to the Middle East to visit with and sing songs of peace for Israel and the Palestinians.

In 1989, after the Tiananmen Massacre in Beijing, Baez wrote and released the song "China" to condemn the Chinese government for its violent and bloody crackdown on thousands of student protesters who called for establishment of democratic republicanism.

In the 1990s, she appeared with her friend Janis Ian at a benefit for the National Gay and Lesbian Task Force, a gay lobbying organization, and performed at the San Francisco Lesbian, Gay, Bisexual and Transgender Pride March.

In 1993, at the invitation of Refugees International and sponsored by the Soros Foundation, she traveled to the war-torn Bosnia and Herzegovina region of former-Yugoslavia in an effort to help bring more attention to the suffering there. She was the first major Artist to perform in Sarajevo since the outbreak of the Yugoslav civil war.

In October of that year, Baez became the first major Artist to perform in a professional concert presentation on Alcatraz Island (a former U.S. federal prison) in San Francisco, California, in a benefit for her sister Mimi's Bread and Roses organization. She later returned for another concert in 1996.

On Earth Day 1999, Baez and Bonnie Raitt honored environmental Activist Julia "Butterfly" Hill with Raitt's Arthur M. Sohcot Award in person on her 180-foot (55 m)-high redwood treetop platform, where Hill had camped to protect ancient redwoods in the Headwaters Forest from logging.

Beginning in 2001, Baez has had several successful long-term engagements as a lead character at San Francisco's Teatro ZinZanni. In August 2001, Vanguard began re-releasing Baez's first 13 albums, which she recorded for the label between 1960 and 1971. The reissues, being released through Vanguard's Original Master Series, feature digitally restored sound, unreleased bonus songs, new and original artwork, and new liner-note essays written by Arthur Levy. Likewise, her six A&M albums were reissued in 2003.

In August 2003, she was invited by Emmylou Harris and Steve Earle to join them in London, UK, at the Concert For a Landmine-Free World.

In the summer of 2004, Baez joined Michael Moore's "Slacker Uprising Tour" on American college campuses, encouraging young people to get out and vote for peace candidates in the upcoming national election.

Baez discussed her relationship with Dylan in Martin Scorsese's documentary film No Direction Home (2005), and in the PBS American Masters biography of Baez, How Sweet the Sound (2009).

On May 23, 2006, Baez once again joined Julia "Butterfly" Hill, this time in a "tree sit" in a giant tree on the site of the South Central Farm in a poor neighborhood of downtown Los Angeles, California. Baez and Hill were hoisted into the tree, where they remained overnight. The women, in addition to many other Activists and celebrities, were protesting the imminent eviction of the community farmers and demolition of the site, which is the largest urban farm in the state. Because many of the South Central Farmers are immigrants from Central America, Baez sang several songs from her 1974 Spanish-language album, Gracias a la Vida, including the title track and "No NOS Moverán" ("We Shall Not Be Moved").

In February 2007, Proper Records reissued her live album Ring Them Bells (1995), which featured duets with artists ranging from Dar Williams and Mimi Fariña to the Indigo Girls and Mary Chapin Carpenter. The reissue features a 16-page booklet and six unreleased live tracks from the original recording sessions, including "Love Song to a Stranger", "You Ain't Goin' Nowhere", "Geordie", "Gracias a la Vida", "The Water Is Wide" and "Stones in the Road", bringing the total track listing to 21 songs (on two discs). In addition, Baez recorded a duet of "Jim Crow" with John Mellencamp which appears on his album Freedom's Road (2007). He has called the album a "Woody Guthrie rock album". The recording was heavily influenced by albums from the 1960s, which is why he invited an icon from that era to appear with him. Also in February 2007, she received the Grammy Lifetime Achievement Award. The day after receiving the honor, she appeared at the Grammy Awards ceremony and introduced a performance by the Dixie Chicks.

Throughout most of her career, Baez remained apprehensive about involving herself in party politics. However, on February 3, 2008, Baez wrote a letter to the Editor at the San Francisco Chronicle endorsing Barack Obama in the 2008 U.S. presidential election. She noted: "Through all those years, I chose not to engage in party politics.... At this time, however, changing that posture feels like the responsible thing to do. If anyone can navigate the contaminated waters of Washington, lift up the poor, and appeal to the rich to share their wealth, it is Sen. Barack Obama." Playing at the Glastonbury Festival in June, Baez said during the introduction of a song that one reason she likes Obama is because he reminds her of another old friend of hers: Martin Luther King, Jr.

On June 25, 2009, Baez created a special version of "We Shall Overcome" with a few lines of Persian lyrics in support of peaceful protests by Iranian people. She recorded it in her home and posted the video on YouTube and on her personal website. She dedicated the song "Joe Hill" to the people of Iran during her concert at Merrill Auditorium, Portland, Maine on July 31, 2009.

She performed at the White House on February 10, 2010, as part of an evening celebrating the music associated with the civil rights movement, performing "We Shall Overcome".

On November 11, 2011, Baez played as part of a musical concert for the protestors at Occupy Wall Street. Her three-song set included "Joe Hill", a cover of the Rolling Stones' "Salt of the Earth" and her own composition "Where's My Apple Pie?"

Baez is a resident of Woodside, California, where she lived with her mother until the latter's death, aged 100, in 2013 in a house that has a backyard tree house in which she spends time meditating, writing, and "being close to nature". She remained close to her younger sister Mimi up until Mimi's death in 2001, and as Baez described in the 2009 American Masters documentary, she grew closer to her older sister Pauline before the latter's death in 2016.

Baez had two sisters — Pauline Thalia Baez Bryan (1938–2016), who was sometimes professionally known as Pauline Marden; and Margarita Mimi Baez Fariña (1945-2001) who was generally better known as Mimi Fariña. To varying degrees, both women were also political Activists and Musicians like their sister. They are also notable for having been married to other American artists - Pauline (briefly) to Painter Brice Marden and Mimi to author and musician Richard Fariña with whom she collaborated for several years.

In 2015, Baez received the Ambassador of Conscience Award.

In 2016, Baez advocated for the Innocence Project and Innocence Network. At each concert, Baez informs the audience about the organizations' efforts to exhonerate the wrongfully convicted and reform the system to prevent such incidents.

In November 2017 as part of a release of documents from the National Archives that were supposed to relate to the assassination of John F. Kennedy, an unsubstantiated 1968 FBI report alleged that Baez was involved in the 1960s in an intimate affair with Dr. Martin Luther King, an accusation described by history professor Clayborne Carson, the Director of the Martin Luther King, Jr. Research and Education Institute and a Stanford University, as "part of a smear campaign" against King.

On 10 February 2018, Baez announced three new German dates for February 2019.