The donation, the largest in league history, follows last week's announcement of the NFL's partnership with the U.S. Army to research brain injuries affecting football players and soldiers, NFL.com reported.
The actions come on the heels of the NFL's motion to dismiss a lawsuit brought by 3,400 ex-players and family members for seeking damages for concussions suffered by players through the years, NFL.com said.
Goodell said the NIH donation and Army partnership have "absolutely nothing" to do with the litigation.
"We've been working on this for a long time. We've funded research going back into the '90s, well before any of that litigation," he said.
The money will be used to help the NIH create a sports and health research program.
NFL Commissioner Roger Goodell told NFL.com the donation "is part of our continuing effort to try to pioneer research that is going to improve the safety of our players and well beyond our players -- in other sports and even beyond sports."
"We wanted to find the answers that we think are so important for either head injuries or long-term cognitive care," Goodell said. "We want to make sure we are doing everything possible to get the best research. And NIH obviously is a leading institution that will pioneer that research, determine where the money is spent, help us find those answers, and make sure that it is available for everybody, just like we have done with all of our research."
Goodell said the league hopes the NFL Players Association will be involved extensively.
"We've had extensive discussions at the NIH with the players association," Goodell said. "They've had separate meetings. We've had discussions as recently as this summer. We all want to try to do what's right to try to make our game safer and other sports safer. And this is part of our ongoing effort."