He died at a New York hospital after a short illness, his grandson said.
Seeger gained fame in The Weavers, formed in 1948, and continued to perform in his own right in a career spanning six decades.
Renowned for his protest songs, Seeger was blacklisted by the US Government in the 1950s for his leftist stance.
Denied broadcast exposure, Seeger toured US college campuses spreading his music and ethos, later calling this the “most important job of my career”.
He was quizzed by the Un-American Activities Committee in 1955 over whether he had sung for Communists, replying that he “greatly resented” the implication that his work made him any less American.
Seeger was charged with contempt of Congress, but the sentence was overturned on appeal.
He returned to TV in the late 1960s but had a protest song about the Vietnam War cut from broadcast.
The lofty, bearded banjo-playing musician became a standard bearer for political causes from nuclear disarmament to the Occupy Wall Street movement in 2011.
In 2009, he was at a gala concert in the US capital ahead of Barack Obama’s inauguration as president.
His predecessor Bill Clinton hailed him as “an inconvenient artist who dared to sing things as he saw them.”
Other songs that he co-wrote included Where Have All The Flowers Gone, while he was credited with making We Shall Overcome an anthem of resistance.
Turn! Turn! Turn! was made into a number one hit by The Byrds in 1965, and covered by a multitude of other artists including Dolly Parton and Chris de Burgh.
Seeger’s influence continued down the decades, with his induction into the US Rock and Roll Hall of Fame in 1996, and he won a Grammy award in 1997 for best traditional folk album, with Pete.
He won a further two Grammys – another for best traditional folk album in 2008 for At 89 and best children’s album in 2010.
He was a nominee at Sunday night’s ceremony in the spoken word category.
He was due to being honoured with the first Woody Guthrie Prize next month, given to an artist emulating the spirit of the musician’s work.
Musician Billy Bragg paid tribute to Seeger’s life via Twitter: “Pete Seeger towered over the folk scene like a mighty redwood for 75 years. He travelled with Woody Guthrie in the 1940s, stood up to Joe McCarthy in the 50s, marched with Dr Martin Luther King in the 60s.
“His songs will be sung wherever people struggle for their rights. We shall overcome.”
Seeger performed with Guthrie in his early years, and went on to have an effect on the protest music of later artists including Bruce Springsteen and Joan Baez.
In 2006, Springsteen recorded an album of songs originally sung by Seeger.
On his 90th birthday, Seeger was feted by artists including Springsteen, Eddie Vedder and Dave Matthews in New York’s Madison Square Garden.
Springsteen called him “a living archive of America’s music and conscience, a testament of the power of song and culture to nudge history along”.
His other musical output included albums for children, while appeared on screen several times as well.
A reunion concert with The Weavers in 1980 was made into a documentary, while an early appearance was in To hear My Banjo Play in 1946.
The band, who had a number one hit with Good Night, Irene in the early 1950s, went their separate ways soon afterwards.
Seeger’s wife Toshi, a film-maker and activist, died aged 91 in July 2013. They leave three children.