And Ashley Young is also staying put despite deadline day interest from China and the Premier League.
But it is the news that England star Rooney will not be allowed to leave the club that is most significant.
The 31-year-old striker is expected to end his United career sooner rather than later – with a summer departure now looking likely.
20 done deals we expect to see on transfer deadline day
Tue, January 31, 2017
Express Sport runs through 20 of the most likely deals we expect to see before the transfer window closes at 11pm
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Here are 20 deals we expect to see before the transfer window closes at 11pm
And a big money offer from China still looks likely to be too good to refuse with figures of up to £1 million a week being bandied around.
Mourinho, however, will not let him leave in the current Chinese transfer window – open until the end of February.
“Yes,” said Mourinho when asked if Rooney will see out the season at Old Trafford.
“We don't have players in, we don't have players out, we lost two players from the squad.
Jose Mourinho wants to keep Wayne Rooney at Manchester United
“You can say Memphis Depay and Morgan Schneiderlin did not play a lot, but the reality is they played some matches, and when they did, others didn't, and when they played, others were rested.
“When Schneiderlin played, it meant Pogba, Carrick or Herrera didn’t.”
Mourinho had thought that Young, a target for China as well as Swansea and West Brom, might be on his way out but not only will the winger stay, but he is in the squad for tomorrow’s clash with Hull.
Mourinho said: “He's staying, he's selected for tomorrow. He stays with me until the end of the season. It's finished.”