"The NFL and our players are at our best when we help create a sense of unity in our country and our culture,” Goodell said in a statement Saturday morning.
“There is no better example than the amazing response from our clubs and players to the terrible natural disasters we've experienced over the last month," he said.
Trump, speaking at a political rally in Alabama Friday night, used profane language while calling on the NFL to fire players protesting racial injustice by kneeling during the national anthem.
“Wouldn’t you love one of the NFL owners, when someone disrespects our flag, to say, ‘Get that son of a (expletive) off the field right now? Out. He’s fired!’” Trump said.
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.