The grievance alleges the league's owners "colluded to deprive Mr. Kaepernick of employment rights in retaliation for Mr. Kaepernick's leadership and advocacy for equality and social justice."
The NFL did not immediately respond to a request for comment.
Instead of filing the grievance through the NFL Players Association, Kaepernick has hired attorney Mark Geragos, who has represented several high-profile clients, including Michael Jackson, former NASCAR driver Jeremy Mayfield and musician Chris Brown.
Geragos said in a statement given first to ABC News Sunday night that the grievance was filed "only after pursuing every possible avenue with all NFL teams and their executives."
Kaepernick's goal, he said, was just to be treated fairly and to return to playing football in the NFL, "the league he performed at the highest level for."
The NFL Players Association said in a statement that it had been in contact with Kaepernick for the past year about his options, but only today learned he had decided to file the grievance, through media reports.
"Our union has a duty to assist Mr. Kaepernick as we do all players and we will support him," the statement said, adding that the union is scheduling a call with his advisers for early this week.
Kaepernick, who has not been with an NFL team since he severed his contract with the 49ers in March, began his silent protest of kneeling during the anthem in the 2016 preseason. He told the media he was protesting against the treatment of blacks in the United States.
Some other NFL players followed his lead during the 2016 season, drawing a mixed response from football fans and the general public, with some supporting the protest and others not.
The president told the crowd at the rally on Sept. 22 that teams should fire players who kneel during the anthem.
In response at NFL games over the next few days, many more players kneeled during the anthem or locked arms with teammates and in some cases also with their team's owners.
In his statement, Geragos did not name the president, but referred to Trump's call for protesting players to be fired, saying: "Athletes should not be denied employment based on partisan political provocation by the executive branch of our government. Such a precedent threatens all patriotic Americans and harkens back to our darkest days as a nation."
ABC News' Sunny Hostin and The Associated Press contributed to this report.