The Ecuadorian defender was not in the United squad for the 3-0 win over Sunderland and was replaced by Matteo Darmian.
While David de Gea was another notable absentee through injury.
But Mourinho believes both injuries are minor and he expects Valencia to be back for the Europa League match in midweek.
Manchester United player ratings against Sunderland
Sun, April 9, 2017
Express Sport rates how the Manchester United players performed during their Premier League clash with Sunderland
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Which Manchester United players impressed during their clash with Sunderland?
Manchester United manager Jose Mourinho
He told BBC Sport: "We had lots of players that were not here today and the most important thing after the three points was to have no more injuries. Only Valencia is the one I really expect to recover and play the next match.
"It's a little De Gea injury. It's not a big problem.
"When he dives to one side he feels a little bit but Romero is very good and very solid and Romero goes again to play in the Europa League."
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