TSA Administrator John Pistole announced the change at a meeting of the Senate Homeland Security and Government Affairs Committee in Washington.
CNN reported Wednesday the change was spurred when a YouTube video showed a TSA screener patting down a six-year-old passenger at the New Orleans airport in April.
Pistole said a female screener searched the young girl after she moved while a body scan was made, making it impossible to determine if she was carrying any banned items.
Sen. Rand Paul, R-Ky., questioned Pistole about the TSA's procedures during the meeting.
"This isn't to say we don't believe in safety procedures," Paul said. "But I think I feel less safe when we're doing these invasive exams on a 6-year-old. It makes me think that you're clueless, that you think she's going to attack our country, and that you're not doing your research on the people who would attack our country."
Pistole said patting down children isn't without merit.
"Unfortunately, we know that terrorists around the world have used children as suicide bombers," Pistole said.