According to the Oakland Tribune, an agreement to dismiss the claim was filed Monday in U.S. District Court. No details of the settlement were released.
Goldieblox filed suit in November, seeking to pre-empt any possible claims of copyright infringement over the re-purposed song.
The video, which shows young girls singing about science and engineering, was viewed millions of times before it was removed from YouTube.
The Beastie Boys countersued Goldieblox in December. The newspaper says it was not immediately clear if Monday's settlement would have any effect on that claim.
The hip-hop group has a blanket ban on using their songs in advertisements.
The two remaining members of the group are Michael "Mike D" Diamond and Adam "Ad-Rock" Horowitz. The third founding member, Adam "MCA Yauch," died in 2012 after a battle with cancer. He was 47.