U.S. District Judge Lewis Kaplan approved a request from federal prosecutors to dismiss the charges, which is a routine procedural move taken when defendants under indictment die.
Bin Laden was indicted in June 1998 in federal court on charges he supported the ambush that left 18 American soldiers dead in Somalia in 1993.
The indictment was later revised to charge bin Laden in the dual bombings of two American embassies in East Africa that killed 224 people in August 1998 and in the suicide attack on the USS Cole in 2000. None of the charges involved the Sept. 11, 2001, terrorist attacks.
The charges included conspiracy to kill U.S. nationals, conspiracy to use weapons of mass destruction against U.S. nationals and conspiracy to damage and destroy U.S. property.
Around the time the charges were first filed, the CIA's bin Laden unit was pursuing a plan to use Afghan operatives to capture bin Laden and hand him over for trial either in the United States or in an Arab country, according to the 9/11 Commission. Bin Laden evaded capture for more than a decade until May 2, when he was killed during a Navy SEALs raid of his compound in Pakistan.
The Associated Press contributed to this report.