Seeger passed away Monday in New York after being hospitalized for a week.
He is also known for popularizing the hymn of the civil rights movement, "We Shall Overcome."
His death was confirmed by his grandson, Kitama Cahill Jackson, who said he died of natural causes at New York-Presbyterian Hospital, the New York Times reported.
Seeger played 12-string guitar or five-string banjo.
He sang topical songs and children's tunes as well as anthems, and often urged his audience to sing along.
In 2009, Seeger performed at a concert in honor of Barack Obama's inauguration, and on Wednesday, the US president paid tribute to the celebrated troubador.
"Pete Seeger believed deeply in the power of song. But more importantly, he believed in the power of community -- to stand up for what's right, speak out against what's wrong, and move this country closer to the America he knew we could be," Obama said in a statement.
"Over the years, Pete used his voice -- and his hammer -- to strike blows for worker's rights and civil rights; world peace and environmental conservation. And he always invited us to sing along."
Pete Seeger sang for the labor movement in the 1940s and 1950s, for civil rights marches and anti-Vietnam War rallies in the 1960s.
He also intoned for environmental and antiwar causes in the 1970s and beyond.
He was a mentor to folk and topical singers in the '50s and '60s, among them Bob Dylan and Don McLean.
Seeger became an icon on college campuses, and at a Madison Square Garden concert celebrating Seeger's 90th birthday, 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."
He won four Grammy Awards, and in 1996 was inducted into The Rock and Roll Hall of Fame, as an early influence.
