The quarterback Colin Kaepernick ignited impassioned debates over race, activism and free expression after protesting police shootings of black men by kneeling during “The Star-Spangled Banner” at National Football League games in 2016.

The president tweeted his anger at him and dozens of other players who also knelt in protest during the national anthem. Some fans boycotted games over the players’ actions, and some boycotted the N.F.L. with the belief that Mr. Kaepernick, who failed to land a job the next season, was being blacklisted for his leadership in the movement.

Now, two and a half years later, Mr. Kaepernick and a former teammate, Eric Reid, have reached a surprise legal settlement with the N.F.L., which they had accused of colluding to keep them out of the league.

In a terse joint statement issued on Friday afternoon, the league and the players’ lawyers said that “the parties have decided to resolve the pending grievances” and that “there will be no further comment.”