Dozens of players at several games across the league chose to kneel during the playing of "The Star-Spangled Banner," in the largest such demonstration since the protests first began in 2016.
The first mass protest took place at the NFL's London game between the Jacksonville Jaguars and Baltimore Ravens at Wembley Stadium.
A large number of players from both teams knelt during the playing of the anthem while others stood with their arms interlocked.
Khan later issued a statement decrying Trump's recent comments as "divisive and contentious."
"That's why it was important for us, and personally for me, to show the world that even if we may differ at times, we can and should be united in the effort to become better as people and a nation," Khan said.
The London protests were emulated across the United States as matches kicked off.
In Foxborough, around 15 members of the Super Bowl champion New England Patriots kneeled during the national anthem.
In Chicago, the Pittsburgh Steelers chose to remain in their locker room during the anthem ahead of their clash with the Bears.
Steelers coach Mike Tomlin, who is black, said the decision was not intended to be disrespectful but rather calculated to "remove ourselves from the circumstance."
"These are very divisive times for our country," Tomlin told CBS television. "For us as a football team, it's about remaining solid."
In Detroit meanwhile, the singer of the national anthem Rico LaVelle dramatically dropped to his knee at the end of his rendition.
At least eight Detroit Lions players were seen kneeling during the anthem while others linked arms ahead of their game with the Atlanta Falcons.
The Falcons players including team owner Arthur Blank also joined arms.
More than 20 Cleveland Browns players kneeled during the anthem for their game against the Colts in Indianapolis.
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