speculation that he could be set to leave the club he joined from Everton in 2004.
However, United manager Alex Ferguson has branded those reports "rubbish" and revealed that the 27-year-old will play a part at Old Trafford on Sunday.
Though he stopped short of confirming that Rooney would start the game, Ferguson defended his right to keep his team selections under wraps.
"He'll be involved on Sunday," the United manager said.
"(But) I'm not prepared to give away my team. Why should I? Why should I help anyone? We don't do that."
Ferguson was nonetheless prepared to reveal that Ryan Giggs will play no part against Chelsea after putting in a superb 90-minute shift against Madrid in what was his 1,000th senior appearance.
"Ryan Giggs won't play (against Chelsea) on Sunday. Why? He was the best player we had (on Tuesday)," said Ferguson.
"We know how to control him and get Ryan prepared for certain games. He has done his bit for us. Next week, yes; different game, another bit of rest.
"Wayne understood exactly what we were doing. I explained to him before we announced the team."
Ferguson was so angered by his side's loss to Madrid, which turned on the controversial 56th-minute dismissal of United winger Nani, that he refused to speak to the media after the game.
He will nonetheless have found solace in United's 12-point lead over Manchester City at the top of the Premier League table, as well as the possibility of reaching a first FA Cup final since 2007.
Chelsea's situation is rather less comfortable.
Winners of the FA Cup in four of the last six seasons, Chelsea's recent form suggests the trophy may represent their only chance of finishing the season with some silverware.
The Blues currently sit in fourth place in the Premier League and suffered a shock 1-0 loss at Steaua Bucharest in the first leg of their Europa League last-16 tie on Thursday.
However, goalkeeper Petr Cech believes the trip to Old Trafford provides a perfect opportunity to draw a line beneath their own European disappointment.
"It's the best way to forget about this defeat," Cech told Chelsea TV.
"The games are coming thick and fast. We won't have much time to prepare, but we'll get a little bit of rest and hopefully we'll have a good performance on Sunday.
"They are the favourites for the game, but it's the FA Cup and in the FA Cup not every time do the favourites win.
"We're still the holders, so we'll try to keep our trophy as long as we can."
Serbian defender Branislav Ivanovic is wary of the threat that a wounded United will present.
"It is going to be one of our biggest challenges of the season, especially playing them at this moment," he said.
"When you go out of the biggest competition in that way, it must be disappointing, but they will be more motivated because of that."
With Giggs sitting the game out, Ferguson is likely to turn to either Antonio Valencia or Ashley Young to fill one of the wide roles.
Phil Jones (ankle) and Paul Scholes (knee) are both definitely out thanks to injury.
Beleaguered interim Chelsea manager Rafael Benitez has rotated his squad in recent games and could elect to omit Fernando Torres and captain John Terry from his starting XI.
Both players started the game in Bucharest, but Demba Ba, Victor Moses and Ramires missed the trip to Romania and are expected to return to the squad.