Obama was addressing a get-out-the-vote rally for Clinton here when the man, wearing a military uniform and hat, stood up in the bleachers and prompted the response from supporters of the Democratic nominee.
"Hold up! Hold up! Hold up! Hold up!" Obama shouted over and over as the supporters drowned out his calls for order.
"Everybody! Hey!" Obama yelled. "I told you to be focused and you're not focused right now."
The President then reminded the crowd "we live in a country that respects free speech," adding the man looked like he possibly served in military, saying, "we ought to respect that."
The episode lasted for more than a minute before the Trump supporter was escorted from the venue.
Trump later on Friday mischaracterized Obama's handling of the protester, accusing Obama of becoming "unhinged" and of "screaming at this protester."
"Frankly, it was a disgrace," Trump said at a rally in Hershey, Pennsylvania.
While Obama reminded his supporters of free speech rights in the US, Trump has on several occasions encouraged violence against protesters at his rallies, including saying he wanted to punch a protester "in the face" and fondly recalling the "old days" when protesters would have been "carried out on a stretcher."
It was Obama's second time in North Carolina in 24 hours. He is scheduled to continue campaigning in the swing state when he visits Charlotte.
Obama spent much of his remarks highlighting the importance of voting, telling the audience, "You got four days to decide the future of this country."
Obama also hit Trump, saying, "We can't have a president who every day seems to violate those basic values."
"It's like suddenly reality TV has entered into the race for the presidency. It's not even 'Survivor' or the 'Bachelorette.' I mean, it's like some 'Love and Hip Hop' stuff," Obama said, raising his eyebrows as the audience laughed.