The lawsuit filed on Wednesday in U.S. Court in Hawaii alleges that Singer, 48, used his influence as a Hollywood insider as well as a range of drugs and alcohol to force anal and oral sex on the boy while promising him roles in his films.
Michael Egan seeks unspecified damages and a jury trial after wide-ranging abuses at California and Hawaii house parties beginning in the late 1990s, according to the civil action.
Singer's attorney, Marty Singer, called the claims "without merit" and "absurd and defamatory."
"It is obvious that this case was filed in an attempt to get publicity at the time when Bryan's new movie is about to open in a few weeks," Singer said in the statement.
"X-Men: Days of Future Past" will open in U.S. theaters on May 23 and is distributed by 20th Century Fox. It is expected to be one of the top-grossing films of the year with a projected opening weekend haul of $103 million, according to Boxoffice.com.
The lawsuit could complicate the global promotion roll-out for Fox by pushing the director's legal problem to the forefront of the film starring Hugh Jackman, Jennifer Lawrence, Patrick Stewart, James McAvoy and Halle Berry.
Singer, who directed "X-Men" in 2000 and its sequel "X2" in 2003, is also signed on to direct the next installment in the franchise, "X-Men: Apocalypse," for Fox, which did not immediately respond to a request for comment. The film is scheduled to be released in 2016.
"X-Men: Days of Future Past" could be a rebound for Singer, whose previous film, "Jack the Giant Slayer," underperformed at the global box office.
The suit accuses Marc Collins-Rector, a former entertainment business executive and registered sex offender, of initiating the sexual abuse by arranging for Singer to meet Egan at "notorious parties" in Encino, California, around 1998.
"The parties were typically sordid and featured sexual contact between adult males and the many teenage boys who were present for the parties," the lawsuit said.
Collins-Rector, who could not be reached for comment, was not listed as a defendant in the suit.
Egan moved to the Los Angeles-area when he was 14 or 15. He was paid at least $1,500 per week by Collins-Rector's former entertainment company without any clear job, as well as sent on private jets "to attractive locations," the suit says.
Egan was also allegedly threatened by Singer and other men who told him they "controlled Hollywood and would destroy his hopes and dreams of an acting career if he did not keep them happy", the lawsuit said.
Egan, then 17, was flown to Hawaii on at least two roughly week-long trips in 1999 where Singer allegedly provided him with drugs and booze and assaulted him in a number of non-consensual sexual acts.
Egan's attorney, Jeff Herman, is noted for his representation of sex abuse victims, having filed suits against the Roman Catholic Church and Kevin Clash, the former voice of Sesame Street character Elmo.