Michael Carrick misses out at Stamford Bridge with the calf problem that forced him off towards the end of Sunday’s derby win over Manchester City, and Van Gaal will also be without Phil Jones (ankle), Daley Blind (ankle) and Marcos Rojo (adductor).
That gives the United manager problems at the back, with Jonny Evans still banned, although left-back Luke Shaw is available for the first time since last month’s FA Cup defeat to Arsenal.
Paddy McNair is the obvious choice to partner Chris Smalling at centre-half, but the absences of Blind and Carrick leave United without a recognised holding midfielder.
That could mean a role for Rooney at the base of Van Gaal’s midfield, a move which would open the door for either Robin van Persie or Radamel Falcao to come in up front.
Neither player has started a game since February, but Falcao has featured regularly as a substitute and Van Persie has been back in training for more than a week after recovering from ankle ligament damage.
“It is the worst scenario,” Van Gaal said. “Marcos and Phil can both play left central defender and Jonny Evans is also suspended so I do not have many choices.
“Daley Blind and Michael Carrick could play as a holding midfield player and I don’t have another option, or I have to play Wayne Rooney again in that position. It is a puzzle.”
United go to Stamford Bridge eight points behind the Premier League leaders, who have a game in hand, and one behind second-placed Arsenal.
And van Gaal, who believes Jose Mourinho would be “satisfied” with a draw on Saturday, says it is “not logical” to think his side can bridge the gap to Chelsea over the remaining six games.
“It is still possible,” he said. “But it is not logical. It is more ‘when and if’, and I don’t believe in ‘when’ and ‘if’ – I believe in facts.
“The fact is now we are behind Chelsea. Alright, we have to play against them and Arsenal have to play against them, so we can lay pressure on Chelsea’s shoulders, and then you never know.
“You have seen it in previous Premier League seasons. I cannot say it is not possible, but it is not logical.”