Neuer, who underwent a minor operation on his left foot following a training-ground injury on March 29, missed Bayern's Bundesliga games against Augsburg, Hoffenheim, and Borussia Dortmund.
Bayern says the chances of Neuer facing Madrid in the first leg of their Champions League quarterfinal are ''good.''
Striker Robert Lewandowski missed Monday's session, instead training individually after taking a knock to his right shoulder on Saturday in the defeat of Dortmund.
Forward Thomas Mueller, who didn't play against Dortmund, says, ''I trained fully normally and that's a good sign.''
Defender Mats Hummels was already ruled out of Wednesday's match due to an ankle injury sustained in training on Sunday.