It was not immediately clear exactly what Trump meant by his remarks, but US media and social media users quickly expressed concern that Trump was advocating, in jest or not, that Clinton or the judges could be shot.
"Hillary wants to essentially abolish the Second Amendment," Trump told a rally in Wilmington, North Carolina, referring to the US Constitution's clause that enshrines the rights of Americans to bear arms.
"If she gets to pick her judges, nothing you can do folks," Trump said. "Although the Second Amendment people -- maybe there is, I don't know."
The Trump campaign swiftly issued its own statement to clarify the brash billionaire's remarks, branding the media as "dishonest" and saying he meant that gun rights advocates were a powerful voting force.
"It's called the power of unification -- 2nd Amendment people have amazing spirit and are tremendously unified, which gives them great political power," senior Trump communications advisor Jason Miller said.
"And this year, they will be voting in record numbers, and it won't be for Hillary Clinton, it will be for Donald Trump."
But Clinton campaign manager Robby Mook blasted Trump for using "dangerous" language.
"A person seeking to be the president of the United States should not suggest violence in any way," Mook said.
The Republican nominee has repeatedly bashed his Democratic opponent for seeking to abolish gun rights.
Clinton has stressed she wants to impose stricter limits on gun sales so that weapons do not fall into the hands of people who should not have them, like criminals, the mentally unstable, or those on government terror watch lists.
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Democratic Senator Chris Murphy of Connecticut, the state where 20 schoolchildren and six adult staff were shot dead by a deranged gunman at an elementary school in 2012, issued a stern rebuke of Trump for his comments.
"Was @realDonaldTrump suggesting his supporters shoot Hillary? Shoot her nominee? Who knows. It's all so disgusting and embarrassing and sad," Murphy tweeted.
"This isn't play. Unstable people with powerful guns and an unhinged hatred for Hillary are listening to you, @realDonaldTrump," Murphy tweeted.
