More than 60 percent of the group's National Council, comprised of some 1,400 delegates, voted in favor of ending the ban, effective January 1, 2014, the group said in a statement. A prohibition on openly gay adult leaders remains in place.
The decision followed weeks of intense lobbying by gay rights activists and members of conservative organizations, many of them church groups that have traditionally formed the backbone of one of the nation's largest youth organizations.
"I'm a happy camper," said Mike Harrison, 71, a former chairman of California's Orange County Boy Scout Council who voted to end the ban. "The process was a very civil debate... There wasn't any uncivilised behavior. People stated their case, passionately and from many different angles."
He said that by Thursday it had become clear that there was a generation change in the organization and that "the younger generation of scouting just don't see it the way the old guard did."
The Boy Scouts' long-standing ban on gay scouts had become a polarizing issue at the center of the debate on gay rights in the United States, where gay soldiers may now serve openly in the military and where gay couples can wed in a number of states.
For months, the Boy Scouts have been caught between two sides in an emotionally charged debate that has seen both supporters and opponents of lifting the ban threaten to withdraw support.
The Boy Scouts has faced heavy pressure on one side from gay rights supporters and some of the major corporate sponsors who provide much of the group's annual funding, and on the other by a variety of major national church groups, who sponsor and support the large majority of troops nationwide.
"I just resigned from my troop," said Chris Collier, 41, a former troop leader in Alabama and Florida who said he would send his Eagle Scout award back to the organization's national office.
"My grandfather earned his eagle award in 1938. I earned mine in 1990. I was hoping my son could earn his when he grew up. I'm sad, but this is their cross to bear. I'm no longer part of the organization. I'll move in a different direction."
Thursday's vote came about three months after the organization's leadership delayed a decision on changing its membership policy to research attitudes toward admitting gays.
About 70 percent of the group's 100,000 Boy Scout units are chartered by faith-based organizations, according to Boy Scouts membership data. Some 22 percent of the units nationwide are chartered by civic organisations, and 7 percent are chartered by educational groups.
One of the major turning points in the debate came earlier this year when the Mormon church - the largest sponsor of scouting troops nationwide - expressed support for ending the ban. The Mormon church charters nearly 38,000 scout troops representing nearly a quarter million scouts.
The next largest faith-based sponsor is the United Methodist Church, which charters about 11,000 scout troops representing about 363,000 scouts. They, too, issued a statement supporting an end to the ban. The Catholic church, which sponsors about 8,400 troops, has taken no official position on the controversy.
While national polls show a growing acceptance of gay rights, an online survey of about 200,000 BSA members, parents and leaders indicated strong support for maintaining the ban, by a margin of almost 2-1.
"The Boy Scouts are not listening to us," said John Stemberger, an Orlando lawyer, Eagle Scout, former scoutmaster and founder of an organization that opposes lifting the ban.
But the Boy Scouts' top leadership had endorsed the change and encouraged delegates to support it. BSA President Wayne Perry said in a webcast: "It was never our intent to prevent young people from being part of this organisation."
Zach Wahls, an Eagle Scout raised by two lesbians, said the time has come for change.
"There is nothing Scout-like about exclusion of other people, and there is nothing Scout-like about putting your own religious beliefs before someone else's," Wahls, founder of Scouts for Equality, told a news conference on Wednesday.
Gay rights advocates gathered petitions with more than 1.8 million signatures in support of ending the ban while opponents collected about 250,000 signatures urging delegates to vote down the change.
Intel Corp, one of the largest corporate sponsors of the Boy Scouts, announced last September that it would stop supporting troops that continue to ban gay scouts. Intel donated about 700,000 dollars in 2009, according to the American Independent magazine.
That announcement followed pressure from gay groups who launched a nationwide campaign on Change.org, urging Intel to withdraw its support. United Parcel Service Inc, another major sponsor, followed suit in November, as did Merck & Co, according to the Gay and Lesbian Alliance Against Defamation.