It was the first Muslim prayer service ever hosted at the National Cathedral in Washington DC with a theme of tolerance.
As the event got underway the woman managed to get through tight security and burst through a door.
"Jesus Christ is on that cross over there, get out of our church. Leave our church alone," she shouted.
Cathedral police had to forcibly remove her allowing the service to continue.
She wasn't arrested and told reporters "I didn't do it for myself, I did it for the Lord."
The service was also condemned by Revd Franklin Graham, the son of U.S. evangelist Billy Graham, who posted on his Facebook page.
He said: "It's sad to see a church open its doors to the worship of anything other than the One True God of the Bible who sent His Son, the Lord Jesus Christ, to earth to save us from our sins.
"Jesus was clear when He said, "I am the way the truth and the life. No one comes to the Father except through Me" (John 14:6)."
The South African ambassador to the United States, who is Muslim, spoke about the threat to the world from Islamist extremism.
"They invade lands, behead journalists, execute civilians and declare war on anyone different to them," he said.