While it is a blow to Manchester United as a club; for whom Rooney has been the focal point of this tour on a marketing basis; as well as Rooney; for whom this could have been an opportunity to prove his worth to the team he has reportedly decided to stay with it is a more significant blow to new manager David Moyes.
While the money-spinning commercial aspect of these tours is well-documented they are of course a chance for managers to reshape and mould their teams; and in the case of a new manager like Moyes to get a sense of how he will enforce his style onto a new set of players.
But it could present him with some other opportunities; at least for their first game against a Singha All-Star XI in Bangkok.
With Rooney’s withdrawal United now only have Danny Welbeck as a recognised striker on the trip. Javier Hernandez has been given the summer off after a busy international campaign while Robin Van Persie will join up with the rest of the team in Sydney.
Shinji Kagawa, who can also play as a withdrawn striker, will also not join up with the team until later on the tour; when they touch down in his Japanese homeland.
So Moyes is left scratching his head in terms of striking options for Thailand.
Obviously he could shift around his formation; playing a 4-3-3 with two midfield players wide of Welbeck for instance.
But it could present an opportunity for him to sample a United new boy up front.
Wilfried Zaha signed for United In January for a fee that could rise above £15 million, but was then loaned back to Crystal Palace, so this tour represents his first real integration with his new team-mates.
While predominantly playing as a winger in his young career so far many believe that Zaha could easily become a forward one day - much like the transition Cristiano Ronaldo made whilst at United.
And Moyes is no stranger to adapting players to a striking position. On a tight budget at Everton he turned Tim Cahill and Maraoune Fellaini into talented advanced men; even pairing the duo during their harder times.
And with Rooney flying home it gives Zaha an early opportunity to show what he can bring through the centre of the field; albeit against a lower class of opposition.
For now his immediate future at United is likely to be as a winger but it is never too early to demonstrate a few extra strings to your bow.
image: © jamesboyes