"The FA will be appealing Wayne Rooney's three-match suspension," a spokesman said on Friday.
"We received a written reason [for the ban] from UEFA on Tuesday afternoon. We had until midnight tonight to respond and we have responded this evening."
As it stands, the suspension would rule Rooney out of the first three matches at next year's European Championships.
Earlier, the Manchester United player said he blamed no one but himself for his "stupid" red card, received after he kicked out at Montenegro defender Miodrag Dzudovic during the match in Podgorica.
Rooney said he would understand if England coach Fabio Capello left him out of the squad for the finals in Poland and Ukraine.
"It was stupid of me and I regretted it as soon as I did it," the 26-year-old told British media. "It's devastating for me but it's something that's my own fault so I can't really complain.
"It's no excuse but I still feel the punishment is a bit harsh. I'm disappointed with it... even if it's reduced by one game it will be a bonus."
Rooney said he had no idea why he acted as he did. England, who were winning 2-1 at the time, went on to draw 2-2 with Montenegro to secure their place in the Euro 2012 finals.
"I honestly don't know why. It was just one of those moments which I live to regret now," he said. "It just happened. I can't explain it.
"I want to be there and be part of the team but I'll understand if I am not in the next squad because I'll be missing the first three games and he [Capello] has to look at other players."
Capello watched Rooney shine in midfield for United in a 2-0 win over Otelul Galati in the Champions League on Wednesday.
"It's probably a role I could enjoy in the future when I've lost a bit of pace," he said. "I played there as a young lad, I understand the role."
