The official online England kit sellers, England-direct.com, told Newsround's website that they were selling loads of shirts with Rooney and number 9 on the back.
Shops in Liverpool - where his club Everton play - are also running out of the last letter of his surname.
But that's not the case in London, where staff at the Soccer Scene shop said David Beckham shirts were still much more popular then ones with Rooney on them.
Online sportswear shop kitbag.com revealed that Rooney is the fourth most popular choice, but he's only been available since the game - around 24 hours.
Other players like Beckham and Michael Owen have been on sale as pre-orders since the end of February!