Jepsen, 27, was one of two headlining acts scheduled to play at the 2013 National Scouting Jamboree in West Virginia in July.
In a tweet Tuesday morning, the Canadian singer said she couldn't participate in an event held by a group with an anti-gay agenda.
The other headlining act, the band Train, has not backed out – but has promised to cancel if the Scouts fail to overturn the ban at a scheduled vote on the matter in May.
Jepsen was apparently swayed by a petition at Change.org started by gay Eagle Scout Derek Nance that specifically urged her not to play the concert. Nance's petition has garnered more than 60,000 signatures.
"I came out as gay because I realized the best way to help end this dangerous policy is to stand up, speak out and tell the organization I love to do the right thing," Nance said in a statement.
"A Scout is brave, and I'm thrilled that Carly Rae and Train have joined me in standing up for what is right," the statement continued. "I hope the Boy Scouts of America also choose to be brave this May."
As an artist who believes in equality for all people, I will not be participating in the Boy Scouts of America Jamboree this summer...— Carly Rae Jepsen (@carlyraejepsen) March 5, 2013