Last week, the 27-year-old put in a transfer request to leave Old Trafford, but he is apparently not on the German champions' radar.
"I don't know what Rooney would bring to the Bundesliga," Bayern's director of sport Matthias Sammer told reporters after recent stories circulated in the German media about the Bavarians' interest in the England ace.
"I can answer that we have great respect for Wayne Rooney, but there has been no contact with him. There is no contact and he's not on the agenda. No, no. Absolutely not."
Bayern have also ruled out any interest in 21-year-old Brazil star and rumoured Barcelona target Neymar.
Ex-Barcelona coach Pep Guardiola already faces an embarrassment of riches when he takes charge next month and must decide who will start in Bayern's star-studded attack with a host of top talent vying for places.
Guardiola will inherit a squad already boasting the likes of Arjen Robben, Franck Ribery, Thomas Muller and Toni Kroos, while Mario Gotze arrives from Borussia Dortmund at the end of the season.
Bayern keen on Ribery extension
Ribery is out of contract in June 2015 and while he has said he wants to extend his deal, the 30-year-old, who has been in superb form as Bayern won this season's German league title for the 23rd time, has yet to sign.
"The door is open for Franck, but he needs to go through it," Bayern chairman Karl-Heinz Rummenigge told Sport Bild. "We have taken note of his words, he is a great player. It's a sign of how good he feels here."