"I don't think that's my decision," Goodell said, saying the decision would instead be made by a former federal judge picked by the commissioner and the players' union to lead the arbitration.
"I think Judge Jones is the one who ultimately is going to make the rules and determinations," Goodell said. "I've been in meetings all day. That isn't something that I've addressed."
The union is appealing Ray Rice's suspension for violating the NFL's personal conduct policy. The former Baltimore Ravens running back was suspended after video of him hitting his then-fiancee in an elevator was publicly released.
Union officials said in announcing the appeal that Goodell and his staff's testimony is a central reason why it pushed to jointly select an outside arbiter.
"The commissioner and his staff will be essential witnesses in the proceeding and thus cannot serve as impartial arbitrators," the NFL Players Association said in a statement.
The appeal will be heard by former U.S. District Judge Barbara S. Jones. Jones is a partner in a private law firm and is also a former Department of Justice attorney.
Goodell said in appointing Jones that she would have "our full cooperation as she hears and decides this appeal."
One month after Rice was initially suspended two games, Goodell said he didn't get things right and announced tougher penalties for future domestic violence incidents. But the penalties didn't apply to Rice.
Once the video was released, the Ravens cut Rice and the league banned him indefinitely, with the league saying it considered the video new evidence.