The England international's last start in the Premier League came during his side's 3-1 defeat to Watford on 18 September. Since then, he has made two starts in all competitions, with the last one coming during the 4-1 Europa League victory over Fenerbahce.
According to Sky Sports, the United captain picked up a muscular injury during training, which will rule him out for the tie against the Blues. Jose Mourinho returns to Stamford Bridge on 23 October for the first time since he was sacked from his post at the west London club last December.
Mourinho assumed charge at the Old Trafford job earlier in the summer and will take his men to Chelsea for the Red Devils' upcoming league clash. It is believed that Rooney has not travelled with the squad to London.
Summer signing Zlatan Ibrahimovic was on the bench and was an unused substitute during the European fixture. The former Barcelona and Paris Saint-Germain striker should return to the starting lineup for the clash against Antonio Conte's side.
It is not certain whether Rooney would have made it to the starting lineup, even if he was fit. But now that he is set to miss the match, Ibrahimovic will be leading United's attack at Stamford Bridge on Sunday.
Meanwhile, Chris Smalling was replaced after the end of the first half by Marcos Rojo against Fenerbahce. Mourinho confirmed the English defender also picked up a "bad muscular injury," but remained hopeful that the centre-back should be fit to face Chelsea.
"He had a bad muscular feeling. We were 3-0 up so we decided to change. Hopefully he can recover for the weekend," Mourinho told United's official website.