"No amount of distance or time will weaken our resolve to bring America's enemies to justice," the Attorney General Eric Holder told reporters in Washington.
The indictment charges Ghaith with participating in a conspiracy to kill US nationals. No trial date has yet been set in the case.
"To violent extremists who threaten the American people and seek to undermine our way of life, this arrest sends an unmistakable message: There is no corner of the world where you can escape from justice because we will do everything in our power to hold you accountable to the fullest extent of the
law," he said.
The arrest of Abu Ghaith is an important "milestone" in our ongoing counter-terrorism efforts, said the Assistant US Attorney General Lisa Monaco.
"It has been 13 years since Abu Ghaith allegedly worked alongside Osama bin Laden in his campaign of terror, and during the period he allegedly took to the public airwaves, exhorting others to embrace al-Qaeda's cause and warning of more terrorist attacks like the mass murder of 9/11," US Attorney, Preet Bharara said.
"The memory of those attacks is indelibly etched on the American psyche, and today's action is the latest example of our commitment to capture and punish the enemies of the United States, no matter how long it takes," Bharara said.
According to the indictment unsealed in a New York Court, from May 2001 to 2002, Abu Ghaith served alongside Osama bin Laden, appearing with him and his then-deputy Ayman al-Zawahiri, speaking on behalf of the terrorist organisation and in support of its mission, and warning that attacks similar to those of September 11, 2001 would continue.
After the 9/11 attack, bin Laden summoned Ghaith and asked for his assistance and he agreed to provide it, it said.
On the morning of September 12, 2001, he spoke on behalf of the al-Qaeda, warning the United States and its allies that "[a] great army is gathering against you" and called upon "the nation of Islam" to do battle against "the Jews, the Christians and the Americans".
Ghaith arranged to be, and was successfully smuggled from Afghanistan into Iran in 2002, where he spent most of the decade.