Rooney trained on Tuesday after missing out on Saturday’s 2-1 win over Watford with illness.
But asked if Rooney would regain his place in the XI, Van Gaal said: “No, not automatically.”
Striker Anthony Martial is also fit, but midfielder Ander Herrera and defender Phil Jones are unavailable.
Marouane Fellaini, who also missed the Watford match, has recovered from a calf injury.
But Van Gaal said the Belgian midfielder, Martial and Rooney would have to “show on the training ground” that they deserved a starting place for the Group B match.
Group B leaders United will go through to the knockout stage with victory, though PSV will have other ideas as they seek the win that could take them top of the section instead.
United were beaten 2-1 in Eindhoven in the reverse fixture and Van Gaal described that match as “very disappointing”, not just because of the result but also because of the loss of Luke Shaw to a broken leg.
“For me and for us he is a very important player,” Van Gaal said. “I said in advance that he would be the revelation of this season and he was on his way to doing that.”
The United manager revealed that he has given Shaw some time off this week from his recovery routine.
“Shaw was fed up with the daily routine and I saw why he was fed up, maybe because it was PSV,” Van Gaal said.
The England international will have a scan on Friday to see how his leg is recovering.
Midfielders Antonio Valencia and Michael Carrick also remain unavailable for United.
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