Fer was sent off by referee Anthony Taylor in the second half of Saturday's third-round 0-0 draw for a cynical trip on Helder Costa.
Swansea manager Carlos Carvalhal said after the game that the foul was a "classic yellow card" and the Premier League club have now confirmed they have taken up the matter with the Football Association.
A statement on the club's website said: "Swansea City have lodged an appeal against Leroy Fer's sending-off at Wolves on Saturday.
"The midfielder was shown a straight red card in the 67th minute of the Emirates FA Cup tie for a foul on Helder Costa which was deemed by referee Anthony Taylor to constitute violent conduct.