"I hear you, I hear you," Obama responded to the heckler.
The heckler continued, and much of the rest of the audience shouted her down.
Obama's speech was interrupted for about a minute as he tried to control the crowd.
"No, no, no, that's fine.Wait, wait...That's okay.Hold on a second. Hold on," Obama said urging people to stay calm.
"Can I just say that as hecklers go, that young lady was very polite. She was. She brought up an issue of importance, and that's part of what America is all about," Obama said.
Manning was sentenced on Wednesday for leaking more than 700,000 pages of classified information to Wikileaks.
On Thursday, 25-year-old Manning said in a statement to the Today Show that he was transgendered, identified as a woman, and preferred to be known as Chelsea Manning.