Wearing a dark blue suit and red tie, Trump, the first sitting or former US president to face criminal charges, sat with his hands folded at the defence table as he entered his plea flanked by his lawyers on Tuesday.
"Not guilty," Trump, 76, said when asked how he pleaded.
He said nothing as he entered the courtroom or when he left roughly an hour later. Trump previously called the charges politically motivated.
He was due to return to Florida and deliver remarks from his Mar-a-Lago resort on Tuesday evening, his office said.
Taken together, the charges carry a maximum sentence of more than 100 years in prison under New York law but an actual prison sentence if he is convicted at a trial would almost certainly be far less than that.
While falsifying business records in New York on its own is a misdemeanour punishable by no more than one year in prison, it is elevated to a felony punishable by up to four years in prison when done to advance or conceal another crime.
The Manhattan grand jury convened by Manhattan District Attorney Alvin Bragg that indicted Trump heard evidence about a $US130,000 ($A192,614) payment made to Daniels in the waning days of the 2016 presidential campaign. Daniels has said she was paid to keep silent about a sexual encounter she had with Trump at a Lake Tahoe hotel in 2006.
Trump's former personal lawyer Michael Cohen has said he coordinated with Trump on payments to adult film actress Stormy Daniels and to a second woman, former Playboy model Karen McDougal. Trump has denied having had sexual relationships with either woman, but has acknowledged reimbursing Cohen.
Bragg, a Democrat, was due to give a news conference later on Tuesday.
Trump earlier held his fist in the air in a gesture to reporters as he departed his New York residence at Trump Tower in a motorcade bound for the courthouse. He exhibited little emotion when he waved to a crowd assembled outside the courthouse.
From his motorcade, Trump posted on social media: "Heading to Lower Manhattan, the Courthouse. Seems so SURREAL - WOW, they are going to ARREST ME. Can't believe this is happening in America."
Trump surrendered to Bragg's office before the arraignment began in Justice Juan Merchan's court. At an arraignment, a defendant hears charges and can enter a plea. Trump was fingerprinted but no mugshot photo was taken, according to a Twitter post by a New York Times reporter.
In other social media posts ahead of the arraignment, Trump renewed his attacks on Merchan, who last year presided over a trial in which Trump's real estate company was convicted of tax fraud.
Trump, who served as president from 2017 to 2021, in November announced a bid to regain the presidency in 2024 in a bid to deny Democratic President Joe Biden, who beat him in 2020, a second term in the White House.
A photo taken by a photographer in the courtroom authorised by the judge showed Trump sitting at the defence table, flanked by his lawyers. Trump's lawyers had urged the judge to block any videography, photography and radio coverage, arguing it would worsen "an already almost circus-like atmosphere."
Any trial is at least more than a year away, legal experts said. Being indicted or even convicted does not legally prevent Trump from running for president.
Trump faces a separate criminal probe by a Democratic local prosecutor in Georgia into whether he unlawfully tried to overturn his 2020 election defeat in the state. He also faces two US Justice Department investigations led by a special counsel into efforts to overturn the 2020 election results and his handling of classified documents after leaving office.
