The Headley case figured at number two in the 10 biggest cases of 2009.
The FBI said, "The threat posed by extremists is real and it continues to morph and evolve in new and dangerous ways."
"We had our hands full during the year, from heading off potential plots on US soil to identifying Americans being recruited to wage jihad overseas," the FBI said in a statement.
Headley was arrested by the FBI in Oct 2009 along with his school-mate Tahawwur Hussein Rana on charges of planning terrorist attacks in India and Denmark.
Headley has also been charged with being involved in the Mumbai terror attack in Nov 2008, which killed more than 170 people including six US nationals.
At the top was the case of the 'Jihadists of Georgia' in which the FBI busted a potential terror plot by two young Americans Ehsanul Islam Sadequee and Syed Haris Ahmed.
"Their story is indicative of both the evolving homegrown extremist threat and the FBI's post 9/11 intelligence-driven investigations," it said.