Rooney was not in manager Louis van Gaal's 18-man squad which travelled to Denmark on Wednesday for the last-32 tie.
"Wayne Rooney is a notable absentee from the flight and the manager is expected to confirm why his captain has not made the trip during his pre-match press conference at 1700 GMT," said a statement on the official site.
Matteo Darmian is another absentee after dislocating his shoulder during the 2-1 Barclays Premier League defeat at Sunderland last weekend.
Adnan Januzaj is cup-tied, having played in the competition earlier this season while on loan at Borussia Dortmund.
Youngsters Donald Love, Will Keane, Regan Poole, Joe Riley and James Weir are all part of the United squad.
United squad: De Gea, Romero, Love, McNair, Smalling, Blind, Poole, Riley, Carrick, Herrera, Schneiderlin, Lingard, Pereira, Weir, Mata, Memphis, Martial, Keane.
Source: PA