"By the way, and if she gets to pick — if she gets to pick her judges, nothing you can do, folks," Trump warned. "Although the Second Amendment people, maybe there is, I don't know."
It was not clear whether Trump was inciting gun owners to use their weapons against judges or a sitting president, or was encouraging some other action.
Trump campaign senior communications adviser Jason Miller released a statement shortly after the comment, swatting down the idea that the mogul was suggesting any form of violence.
“It’s called the power of unification — 2nd Amendment people have amazing spirit and are tremendously unified, which gives them great political power," Miller said in the statement. "And this year, they will be voting in record numbers, and it won’t be for Hillary Clinton, it will be for Donald Trump.”
Clinton's campaign was also swift to respond to Trump's comments.
"This is simple — what Trump is saying is dangerous," Clinton campaign manager Robby Mook said in a statement. "A person seeking to be the President of the United States should not suggest violence in any way."
Sen. Chris Murphy (D-Conn.), a Clinton supporter and staunch gun-control advocate, said on Twitter: "Don't treat this as a political misstep. It's an assassination threat, seriously upping the possibility of a national tragedy & crisis."
Other political candidates have stoked controversy in the past by suggesting that Americans use the Second Amendment to the Constitution to rise up against the government.
For example, Republican Senate candidate Sharron Angle said in 2010 that if Congress "keeps going the way it is, people are really looking toward those Second Amendment remedies and saying, my goodness, what can we do to turn this country around?"
The Second Amendment states: "A well regulated Militia, being necessary to the security of a free State, the right of the people to keep and bear Arms, shall not be infringed."
Some who attended Trump's rally argued that Trump was not trying to incite violence with his comments.
"In no way was he threatening Hillary," said Sarah Smith, a 72-year-old retiree. "Anybody who thinks that is delusional."
Smith said she thought Trump was simply making a comment about the importance of gun rights and the threat posed by judges appointed by the Democratic nominee.
"The Supreme Court is all-important," she said.
James Renaud, 66, said he took the comment "at face value" — meaning gun owners have to mobilize lest Clinton be able to stack the Supreme Court. "It was just off-the-cuff talking."
And Keri Malkin, 49, said she didn't "hear it that way at all," suggesting the insinuation that the comment was a threat against Clinton was engineered by her supporters.
"Hillary lies a lot, so it's no surprise that her supporters would lie," she said.
Here's the video of Trump's comment:
Trump aimed intense criticism at Clinton throughout his rally, labeling her "inept" and accusing her of wanting to raise taxes, leave the nation's borders vulnerable and ramp up hostilities with overseas nations.
"Hillary wants to invade foreign countries," said Trump. At the same time, he argued that a Clinton presidency would expose the country to the threat posed by Islamic State terrorists.
When Trump was interrupted by a protest in the crowd, he accused Clinton's supporters of being responsible and mocked them, saying they lacked the "spirit" shown by protesters partial to her primary rival, Sen. Bernie Sanders of Vermont.
"I like the Hillary protesters, they are so nice and quiet," Trump said.
Sullivan reported from Washington.
This post has been updated.