The National Council of the Boy Scouts of America has voted to allow gay boys to become members.
The ban on adult homosexuals becoming Scout leaders still stands.
The resolution permitting openly gay youths to become scouts was adopted after securing a 61% vote in favour among the National Council's 1,400 members.
The decision has been met with disappointment among American faith groups.
The Assemblies of God said in a statement that it "regrets" the outcome of Thursday's vote.
It added that it could no longer endorse its young members joining the BSA and would instead be encouraging them to become part of its own similar programme, the Royal Rangers.
"We believe – as do a majority of Boy Scout volunteer leaders and parents – that this is not the best policy for BSA, nor for the young men it serves," the Church said.
"We believe that the BSA policy change will lead to a mass exodus from the Boy Scout programme, as Assemblies of God and many other churches can no longer support groups that are part of an organisation allowing members who are openly homosexual."
The president of the executive committee of the Southern Baptist Convention, Frank Page, told the Baptist Press he was "deeply saddened" by the change.
"We know that the pressures exerted against the voting members of the 1,400 chartered organisations by homosexual activist groups have been unrelenting," he said.
"We are grateful for each voting member who voted in the minority; but our sadness for the Scouting organisation as a whole cannot be overstated."
He went on to say that the vote "ushers in a sea-change in the credibility of the Boy Scouts of America as a viable boys' organisation for millions of Americans who believe strongly in the principles of biblical morality".
"We continue to pray for our country. We believe we are in desperate need of a genuine spiritual awakening that will transform lives through the power of the Gospel of our Lord Jesus Christ," he said.