Khan, whose speech was so well received by the audience it seemingly took him aback, challenged Trump throughout his remarks, culminating in a flurry of questions about who would "have a place" in Trump's America.
"So today, I have a few questions for Donald Trump. Donald Trump, would my son have a place in your America?" asked Khan, a Muslim. "Would Muslims have a place in your America? Would Latinos have a place in your America? Would African-Americans have a place in your America, Donald Trump?"
He continued: "Would anyone who isn't you have a place in your America? Well, thankfully, Mr. Trump, this isn't your America."
Khan's son, Army Capt. Humayun Khan, died in Iraq in 2004 and his story -- told by his father at the Democratic National Convention in July -- spurred Trump to attack Khan and his wife, Ghazala. The race was a defining moment in the campaign.
Last month, Khan cut an emotional ad
for the Clinton campaign, in which he also asked Trump if his son would "have a place in your America."
Along with making controversial public comments about a variety of groups during his campaign, Trump also called for a "Muslim ban"
in December. He has since amended the plan to bar entry for people from countries with heavy terrorist activity, though he has never specified which states he's referring to.
Clinton, hours before polls open across the country, described the race in dramatic terms throughout her final event in New Hampshire.
"Our core values are being tested in this election," Clinton said. "This election is a moment of reckoning. It is a choice between division and unity. Between strong, steady leadership or a loose cannon who could put everything else at risk."
She added, "This is one of these elections that really is a crossroads election in our country."
Clinton said that Khan and his family "exemplify the values that make America great" and that all Americans would be "grateful that this remarkable family decided to make American their home."
Clinton's late visit to New Hampshire, while somewhat unexpected by some Democrats in the state, is part of the campaign's strategy to focus on "gameday voting states" -- places where most voting happens on Election Day -- now that early voting has stopped.
"Don't leave it to chance. Don't leave it to others. Use your voice and your vote," Clinton said.
In addition to New Hampshire, Clinton will visit Michigan and Pennsylvania on Monday to close out her presidential campaign, two states where almost all voting happens on Tuesday.
New Hampshire was not friendly to Clinton during the primary. Bernie Sanders trounced the former secretary of state by 22% in February, a fact Clinton noted on Sunday.
"I have to say," Clinton said with a smile, "you all cleaned my clock in this primary."