The Portuguese midfielder picked up the injury in the second half of the 3-0 fifth round replay win at the City Ground.
Coach Chris Hughton reported: "Pedro has fractured a bone in his toe and with it just happening last night we're waiting for reports as to how long that will keep him out. I think we're talking weeks though.
"It just happened in a tackle, one of those things that happen in a game."
Chris added it was blow for Pedro in what was his first start since the 3-0 defeat at Palace on January 22.
"He played well as well," said Chris. "He's a good player and that shows the quality we have in that midfield area. We've been fortunate not to have too many injuries in that area but this is unfortunate for him."
We'll have full team news tomorrow...
Pedro Mendes is facing a spell on the sidelines after fracturing a toe in the FA Cup replay win against Forest.