Sheen described the story as part of an "egregious, hurtful and disgusting campaign of defamations."
Actor Dominick Brascia told the publication that Sheen sexually abused Haim on the set of their 1986 movie "Lucas." The story also quoted an anonymous source claiming Sheen, then 19, "bullied the child actor into a vulnerable position for sex."
Sheen said the story was part of an "egregious, hurtful and disgusting campaign of defamations."
"With calculated malice and the National Enquirer has concluded that it can make money by running false and salacious stories claiming that Mr. Sheen is a sexual molester that preys on young pubescent boys," said the lawsuit obtained by TMZ.
The lawsuit also states Dylan Howard, the Enquirer's editor-in-chief, published the story as his way of getting revenge on the actor for not getting the exclusive on Sheen's HIV-positive status.
The Enquirer's parent company, American Media Inc. said they "look forward to litigating against Charlie Sheen, and can't wait to expose his depravities in a court of law."
The publication also said they have "dozens of other sources" who can confirm their story, but Sheen's lawyer, Shane Bernard, dismissed the claim.
"I think it goes without saying that lies of this nature, especially ones that are meritless and so outright false will not be tolerated," Bernard said.
Haim's mother also dismissed the allegations Sheen sexually abused her son on "The Dr. Oz Show," accusing Brascia of performing the sex act on Corey.