Ghailani, an accused al Qaeda operative, was facing 286 separate counts for his alleged role in the deadly bombings of the U.S. embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya on Aug. 7, 1998.
The Tanzanian national was held at the detention facility at Guantanamo Bay, Cuba, from September 2006 until he was transferred to New York in June 2009 to face trial in a civilian court.
Ghailani originally was indicted in 1998. The superseding indictment, for which he is facing trial, was returned in March 2001.
Captured in July 2004 in Pakistan, Ghailani was part of the CIA's High Value Terrorist Detainee Program before being transferred to Guantanamo Bay.
Ghailani's prosecution showed the complexity of trying former CIA terrorism detainees in civilian courts.
U.S. District Court Judge Lewis Kaplan denied prosecutors from allowing their key witness, Hussein Abebe, to testify. Kaplan ruled that the information that led to Abebe's arrest in August 2006 was obtained from Ghailani while he was in the CIA's program and exposed to enhanced interrogation techniques.
"There's no question," said Jim Cohen of Fordham Law School, "[that] they [prosecutors] were hamstrung" by Kaplan's ruling.
"One of the things we should read into it is juries are not necessarily going to be so appalled by the crime itself that they will give unfair consideration to the defendant," Cohen added. "It shows a detainee charged with these sorts of crimes can get a fair trial in the civil system."
The verdict came two days after a note from one of the jurors indicated that she wanted to be removed from the deliberations and noting that she felt she was being "attacked" by other jurors.
ABC News' Ariane de Vogue, Michael S. James and Shimon Prokupecz contributed to this report.