Rooney, who was named by Roy Hodgson in his England squad to face Scotland next Wednesday when it was unveiled today, is yet to play a competitive game during United's pre-season programme.
And as he will also miss Rio Ferdinand's testimonial against Seville on Friday, he was keen to get a more strenuous workout than the light session planned for David Moyes' first team, Press Association Sport understands.
It explains why Rooney was with the reserves, which has been latched on to by some as further evidence of a worsening relationship with the Old Trafford club.
However in this instance, that is thought not to be the case with the player himself keen to underline the development was at his request, which could yet assist him in appearing against Scotland.
Rooney's selection by England is interesting though.
He has missed all six United pre-season matches so far, having flown home from Thailand less than 24 hours after his arrival due to a hamstring injury, then picked up a minor shoulder problem that prevented him from travelling to Stockholm for Tuesday's encounter with AIK.
Roy Hodgson is due to speak to the media this afternoon to explain his reasoning.
However, given Sir Alex Ferguson's previous assertions that Rooney needs two weeks to get fit if he misses one, Moyes may welcome the chance of a competitive game for the forward, which Wednesday's first meeting with Scotland since 1999 certainly will be.