"Victoria Police can confirm that it has today charged a 33-year-old man from Cheltenham with four counts of rape following an alleged incident in 2004," police said in a statement.
Media widely named the man as Stephen Milne, who has previously protested his innocence.
Police said the decision to lay charges followed an extensive review of the initial investigation by the Sexual Crimes Squad at the request of the office of public prosecutions.
"It is a matter of regret that this review found the initial investigation to have been substantially inadequate," said police.
Milne and another player were investigated but not charged following sexual assault allegations made by two women in 2004.
St Kilda are currently languishing at 16th in the 18-team AFL league table.