More than 60 percent of the 1,400 voting members supported the plan at the annual conference in Grapevine, Texas.
It's a landmark decision for the organization with more than 2.5 million youth members.
Liberal Scout leaders supports the proposal to accept gay youth, though they have made clear they want the ban on gay adults lifted.
Conservatives with the Scouts - including some churches that sponsor Scout units - wanted to continue excluding gay youths. In some cases they threatened to leave the organization if the ban were lifted.
"We are deeply saddened," said Frank Page, president of the Southern Baptist Convention's executive committee after learning of the result. "Homosexual behavior is incompatible with the principles enshrined in the Scout oath and Scout law."
The Assemblies of God, another conservative denomination, said the policy change "will lead to a mass exodus from the Boy Scout program."
But Pascal Tessier, a 16-year-old boy from Maryland, was elated by the outcome. He was a Boy Scout for nearly a decade then announced he was gay and was told he would not earn the highest rank. That is now changing.
"It's actually great. They are finally taking a step in the right direction with allowing gay youth," said Tessier.
The result was welcomed by many gay-rights groups, which joined in the call for an end to the ban on gay adults.
"I'm so proud of how far we've come, but until there's a place for everyone in Scouting, my work will continue," said Jennifer Tyrrell, who's ouster as a Cub Scout den leader in Ohio because she is lesbian launched a national protest movement.
The BSA could also take a financial hit. Many Scout units in conservative areas fear their local donors will stop giving if the ban on gay youth is lifted.
The Boy Scouts of America released a statement, which read in part, "The Boy Scouts of America will not sacrifice its mission, or the youth served by the movement, by allowing the organization to be consumed by a single, divisive, and unresolved societal issue. As the National Executive Committee just completed a lengthy review process, there are no plans for further review on this matter."
The policy change will go into effect Jan. 1, 2014.
The Associated Press contributed to this report.