The president, who also drew some cheers from the audience as he entered the New York arena, attended the event alongside his two sons Donald Trump Jr and Eric Trump and a slew of congressional Republicans.
Several posters saying “Impeach Trump” and “Remove Trump” could be seen in the Manhattan crowd.
The boos come just days after Mr Trump, who is battling a Democrat-led impeachment inquiry, was hit with boisterous boos when he went to a World Series baseball game in Washington DC.
The world leader was greeted with shouts of “lock him up” when he was broadcast on the video screen in Nationals Park.
Trump supporters and protesters opposed to the president’s agenda assembled outside Madison Square Gardens on Saturday night.
Anti-fascist activists were among them and protesters could be heard chanting “Out now!”
Mr Trump, who was sitting several rows from the cage where the mixed martial arts brawl took place, has an established relationship with UFC and its president Dana White is a supporter of the president. The US leader is the first ever sitting president to go to a MMA event.
The visit to New York comes just after the president, who was born and brought up in the NYC borough of Queens, announced he was a resident of Florida.
The New York Times indicated he may be relocating for tax purposes.
Mr Trump claimed he had been “treated very badly” by political leaders in New York in a tweet which declared the move.
He said: “Despite the fact that I pay millions of dollars in city, state and local taxes each year ... Few have been treated worse”.
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