"I'm stunned," McGrath, 49, told The Associated Press on Tuesday. "Our hope is that they'll rethink their decision."
McGrath, who earned the rank of Eagle Scout, has been leading Seattle Troop 98 since its formation was approved last fall. He has taken the small troop to camp in a snow cave at Mount Rainier National Park, and they've worked on knots and lashing skills.
McGrath said the pastor of Rainier Beach United Methodist Church, the chartering organization, asked him to lead the troop, and they submitted an application that was approved by the Chief Seattle Council and national headquarters.
"We were transparent," he said. "If they didn't want us to be a troop, they shouldn't have accepted our application. To hear claims that this is surprising to them is confusing. We've been transparent from day one."
A call to the Chief Seattle Council was not immediately returned Tuesday.
The Boy Scouts began accepting openly gay members for the first time this year, over the objections of some participants who eventually left the organization. Gay-rights groups applauded the move, but it angered people who consider homosexuality a sin and a violation of Scouting values.
The Boy Scouts said it would continue to exclude openly gay adults from leadership positions.
"The Boy Scouts of America does not proactively inquire about the sexual orientation of our members. We don't believe the topic of sexual orientation has a role in Scouting and it is not discussed unless it is deliberately injected into Scouting," BSA spokesman Deron Smith said in an emailed statement Tuesday.
But McGrath provided information to national leadership and the media that led to his removal as a leader, Smith said.
The Rev. Monica Corsaro at Rainier Beach United Methodist Church said she and her congregation are standing by McGrath as troop leader.
"This is a nonissue here. We've gotten no complaints from parents," she said. "He decided to tell his story to somebody is why he's getting in trouble."
Corsaro said Tuesday that she hasn't gotten official word that McGrath is not a Boys Scouts leader, so he'll continue in his role.
McGrath, a software engineer who married his longtime partner in 2008 in California, grew up in Seattle. He was a Cub Scout, became a Boy Scout at 11, and with his twin brother earned Eagle Scout rank before turning 18.
"Scouting was the best part of our youth and adolescence," McGrath said, adding that he, his brother and his dad went to the woods and canoed, and he climbed Mount Rainier for the first time at age 13. "Adolescence was a hard time, but that wasn't. That was uncomplicated and wonderful in every way."
When McGrath came out to his family and friends in 1988 at age 23, the hardest part was anticipating and expecting rejection from the Boys Scouts, he said.