"There is no escape from the reach of our law for violent terrorists, especially if they target our military," said Loretta Lynch, US attorney for the eastern district of New York.
Saddiq al-Abbadi, 36, and Ali Alvi, 30, were arrested on a US warrant in Saudi Arabia for conspiracy to murder Americans abroad and providing material support to Al-Qaeda.
They were extradited to New York where they face trial and life behind bars.
The US government alleges that the pair are members of al-Qaeda who worked alongside the Taliban to attack US troops in eastern Afghanistan in 2008.
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New York prosecutors also accuse Abbadi of fighting against US forces in Iraq from 2003 to 2007.
In March 2008, the pair allegedly travelled from Yemen to Pakistan's northwestern border areas with Afghanistan to train with and fight for Al-Qaeda.
They are accused of helping an American man from Long Island -- who has testified against them -- to join Al-Qaeda.
Abbadi is said to have led a battle against US forces in eastern Afghanistan that May that killed one US Army Ranger and left several others seriously wounded.
"Abbadi and Alvi may have operated in the mountains of Afghanistan but now they face justice in a courtroom in Brooklyn," said Lynch, President Barack Obama's nominee to be the next US attorney general.
The US national they allegedly helped is Bryant Neal Vinas, who travelled to Pakistan and who has been accused of plotting to attack the Long Island Rail Road in New York.