The Eagles, who won their first-ever Super Bowl title in February, were planning to send a small delegation of fewer than 10 players, according to US media outlets.
That decision earned the ire of Trump, who uninvited the entire team from Tuesday’s planned event.
White House officials said that a separate event for more than a 1,000 invited fans would continue regardless.
On Twitter, the US president linked the boycott to the ongoing controversy over anthem protests in US sports.
“The Philadelphia Eagles Football Team was invited to the White House. Unfortunately, only a small number of players decided to come, and we canceled the event,” Trump wrote.
“Staying in the Locker Room for the playing of our National Anthem is as disrespectful to our country as kneeling. Sorry!”
In recent years, a number of US sportsmen and women have taken part in protests during the playing of the anthem by taking a knee or sitting it out.
The protests began when San Francisco 49ers quarterback Colin Kaepernick started kneeling during the anthem in protest at what he called “systematic oppression” of African Americans, of which he said “police violence” was a symptom.
The Guardian documented more than 1,090 police killings in 2016. Nearly a quarter of those killed in 2016 were African American, although the group accounts for roughly 12 percent of the total US population.
Other players began participating in the protests and activists defended the act as an expression of free speech.
However, the protests drew anger from many conservatives, including Trump.
“At least 24 players kneeling this weekend at NFL stadiums that are now having a very hard time filling up,” he tweeted in November last year, adding “The American public is fed up with the disrespect the NFL is paying to our Country, our Flag and our National Anthem. Weak and out of control!”
In May, the NFL announced fines for teams whose players refused to stand for the anthem before games, a move Trump has called “as bad as kneeling”.
Monday’s decision to rescind the White House invite has prompted an angry response.
Philadelphia’s Mayor Jim Kenney condemned Trump’s decision and said the US leader was “not a true patriot”.
“These are players who stand up for the causes they believe in and who contribute in meaningful ways to their community,” he said in a statement.
“They represent the diversity of our nation, a nation in which we are free to express our opinions.
“Disinviting them from the White House only proves that our President is not a true patriot, but a fragile egomaniac obsessed with crowd size and afraid of the embarrassment of throwing a party to which no one wants to attend.”
The Philadelphia Eagles also posted a statement.
“We are truly grateful for all of the support we have received and we are looking forward to continuing our preparations for the 2018 season,” the team said.
— Philadelphia Eagles (@Eagles) June 5, 2018