Roger Goodell admitted the NFL was "wrong" not to listen to its players earlier about racism concerns.
A day after a group of players, led by Kansas City Chiefs star Patrick Mahomes, sent a powerful message to the NFL, Goodell responded.
It comes amid protests across the United States in the wake of the death of George Floyd, who died in police custody in Minneapolis last week.
Former San Francisco 49ers quarterback Colin Kaepernick started kneeling during the United States national anthem in 2016 in protest against racial injustice and police brutality.
In a video posted on social media on Friday, Goodell acknowledged the NFL should have listened to its players earlier.
"It has been a difficult time for our country, in particular black people in our country. First, my condolences to the families of George Floyd, Breonna Taylor, Ahmaud Arbery, and all the families who have endured police brutality," he said.
"We, the National Football League, condemn racism and the systematic oppression of black people. We, the National Football League, admit we were wrong for not listening to NFL players earlier and encourage all to speak out and peacefully protest. We, the National Football League, believe black lives matter.
"I personally protest with you and want to be part of the much-needed change in this country. Without black players, there would be no National Football League and the protests around the country are emblematic of the centuries of silence, inequality and oppression of black players, coaches, fans and staff.
"We are listening, I am listening and I will be reaching out to players who have raised their voices and others on how we can improve and go forward for a better and more united NFL family."