While most of United's top players were benched or rested entirely for the English League game against third-tier Northampton on Wednesday, Rooney played the full 90 minutes less than three days before a big Premier League match against champion Leicester.
There could be two explanations for this selection: Mourinho either wanted his captain out on the field to lead the team in a potentially tricky away cup tie; or there's a chance Rooney could be left out at the weekend.
In a terse television interview before the Northampton game, Mourinho was twice asked what he wanted from Rooney.
"Goals," came the reply from the stern-faced Portuguese coach, both times.
United won 3-1 but Rooney, who started the match as a central striker before dropping deeper in the second half, did not score.
The Rooney dilemma where to play him, if at all is hanging over Mourinho and won't go away, because it's the most hotly debated issue in English football at present.
Rooney was restored to his favored No 10 position by Mourinho for this season, after finishing last season as a central midfielder for United and England's national team.
But it remains questionable if he is doing enough to justify his place, and if this positional switch might be stifling the effectiveness of world-record signing Paul Pogba and new star striker Zlatan Ibrahimovic.
Pogba is being played as one of two deep-lying players in central midfield, with Rooney ahead of him, even though the France international is better suited in a three-man midfield that allows him more freedom to attack and not be overly concerned with his defensive responsibilities similar to how he played at Juventus.
It seems strange to spend USD 116 million on a player and not adapt the team to his strengths.
Ibrahimovic, meanwhile, is a center forward who likes to roam where he wants, and he enjoyed huge tactical freedom at Paris Saint-Germain, his former club.
But his tendency to improvise on a whim can also unbalance teams. For example, if Ibrahimovic is dropping deep to get more involved in play then that space is already being occupied by Rooney.
Given the presence of Pogba and Ibrahimovic, a 4-3-3 formation with no authentic No. 10 could be the way forward for United.
Rooney, who has been at United since 2004, has had his moments this season, notably setting up Marcus Rashford for a last-minute winner at Hull and also supplying a brilliant right-wing cross that Ibrahimovic headed home in a victory against Southampton.
He still has an excellent football brain, a good range of passing, and an exemplary work rate. Critics, though, argue Rooney has lost his pace and explosiveness, and therefore is slowing down United's attacking tempo. He had a particularly disappointing game in United's 3-1 loss at Watford on Sunday, its third defeat in a row over nine days.
Here are Mourinho's options going forward regarding Rooney:
Keep Him As No. 10
Rooney is United's and England's captain and needs four more goals to become the club's all-time record scorer, topping Bobby Charlton's 249 goals.
Given time, he might improve his partnership with Ibrahimovic, while Pogba might learn how to better operate in a midfield two. Rooney hasn't been among the players publicly criticized in recent weeks by Mourinho, who has long been a fan of the player.
Rooney finished the Northampton game on the right of a front three also containing Ibrahimovic and Rashford. He is hard-working, has played the wide role before, and United's other wingers Anthony Martial, Jesse Lingard and Memphis Depay are hardly in the best form.
Maybe Rooney could stay there, as part of a 4-3-3 formation or with a teammate like Juan Mata or Henrikh Mkhitaryan in the No. 10 role. Then again, Mourinho said in his first news conference as United manager: "For me, he will be a nine, he will be a 10, he will be a nine-and-a-half." That suggests Rooney will be a central striker or a deep-lying striker.
The last manager to drop Rooney was Alex Ferguson, in the final season of his near-27-year reign. It almost led to Rooney leaving United. Mourinho could do the same in an attempt to get more out of Pogba, give Ibrahimovic more space to rove in attack, and inject some more pace into the forward line.
Over at Manchester City, Pep Guardiola has shown his tough streak in dropping two club greats in Joe Hart and Yaya Toure early in his tenure. Is Mourinho ready to make a similar statement?