Brady did say he hopes to make another White House visit following another Super Bowl title.
The 27-year-old was no stranger to the White House, having visited former president Barack Obama after the Super Bowl XLIX win in 2015.
Six other Patriots had announced they wouldn't attend the event for political reasons.
But other members of the team had a bit of fun during the visit, including tight end Rob Gronkowski, who crashed Press Secretary Sean Spicer's daily press briefing. Hernandez was serving life in prison for the 2013 murder of Odin Lloyd.
On Wednesday morning he explained his decision in a statement that read, "I am so happy and excited that our team is being honored at the White House today". "No team has been this good for this long", the president said.
Trump's welcome to the team was coming hours after the news from MA prisons officials that ex-Patriot tight end Aaron Hernandez hanged himself in his prison cell.
American, Russian arrive at International Space Station
The rocket lifted off at 3:13 am EDT/ 7:13 GMT with a rare empty third seat from the Baikonur Cosmodrome in Kazakhstan. The two American astronauts are scheduled to speak with President Donald Trump on Monday.
"I wouldn't spend time away from my family to shake the hand of a guy I wouldn't want to meet with or talk to", Branch told the Boston Globe.
Gronkowski asked him if he was sure, and when Mr Spicer reiterated his initial response, he told him he'd let him get on with it, to which Mr Spicer said: "Alright, thanks man".
One player made an impromptu appearance at a White House press before the official ceremony.
Despite Trump's claims at a New Hampshire rally that Brady said, "Donald, I support you, you're my friend and I voted for you", his wife Gisele Bündchen denied they supported the president.
During the South Lawn ceremony, Trump recounted reading a supportive letter from Belichick on the eve of the election, while Kraft saluted the president as a friend for decades.
"I've had the great privileged to be here several times, but this one, th way we were treated the opportunity to be in the Oval Office and be with the President, and see the inside of the White House, has just been fabulous", Belichick said of Wednesday's visit.
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