A news release said $60 million will go toward improving helmets for players, and the remaining $40 million will help fund medical research into the effects of head injuries.
Goodell told The Washington Post that the initiative "builds on what we've done the last few years but it takes it to another level in a variety of areas ... It's all about protecting our players."
The announcement came almost a week after Carolina Panthers quarterback Cam Newton suffered multiple helmet-to-helmet hits against the Denver Broncos.
Only one of those hits was penalized, and many were surprised that Newton didn't undergo concussion testing-procedures during the game.
The NFL has previously donated to medical research. It gave the National Institutes of Health $30 million in unrestricted funding in 2012.
That decision came under fire after a congressional report accused the league of trying to influence how the money was used.
Goodell also promised to hire a full-time chief medical officer by the end of the season.
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