Goodell said Trump's comments show an ignorance of what the NFL stands for and what it means to be a football player.
"Divisive comments like these demonstrate an unfortunate lack of respect for the NFL, our great game and all of our players, and a failure to understand the overwhelming force for good our clubs and players represent in our communities," the commissioner said.
Trump also blamed the protests for lower NFL ratings this season, contending that they have negatively affected the game.
Former San Francisco 49ers quarterback Colin Kaepernick first started kneeling during the national anthem last year to protest police violence against minorities. Since then other NFL players have joined in the protests, and players in other sports have, too.