According to The Sun, the former England international - who recently became a dad for the fourth time - has been informed that he must pay back £5m.
Rooney is said to have taken advice from a trusted expert on the scheme, which reduced tax bills by claiming against early losses on blockbusters that later made money.
A source is quoted by the publication as saying: "Wayne is furious. He followed advice by so-called experts to make investments. Now years later the taxman's after him for millions he's said to owe. It's ridiculous and unfair."