"I think he probably means well," the GOP presidential candidate said on Fox News' "Fox & Friends" on Wednesday.
Trump was reacting to Obama's speech on Tuesday announcing new executive actions on guns, including narrowing the so-called "gun-show loophole" on background checks.
The Republican front-runner said what the President gets wrong is "the concept" behind his efforts, not his emotion.
The President grew emotional during his remarks, with tears falling down his face as he talked about the first graders massacred at Sandy Hook Elementary three years ago.
Trump said those tears were real.
"I actually think he was sincere, I'll probably go down about 5 points in the polls by saying that, but I think he was sincere," Trump said.
But the mogul reiterated his frequent position that the answer to mass shootings is having more people with guns in the room, not fewer.
And, looking ahead to the presidential race, Trump attacked other Democrats and front-runnner Hillary Clinton alongside Obama.
"His idea is just taking chunks and chunks out of the Second Amendment until we don't have a Second Amendment anymore, and people need protection," Trump said. "Hillary Clinton is, I think, worse than Obama on the issue, frankly, she wants to take everyone's gun away."
Later Wednesday, Trump told CNN's Wolf Blitzer on "The Situation Room" that Obama should take action to protect Americans, but through legislation, not executive action.
"We have to protect the Second Amendment," Trump told Blitzer. "We have no choice. We have to do that."