Seale died Tuesday in Terre Haute, Ind., where he had been serving three life sentences after being convicted in 2007, Bureau of Prisons spokesman Edmond Ross told The Associated Press. He was 76.
Ross said he did not know the cause of Seale's death, which was first reported by Jackson newspaper The Clarion-Ledger.
Seale was convicted of two counts of kidnapping and one of conspiracy to commit kidnapping in the 1964 deaths of Henry Hezekiah Dee and Charles Eddie Moore, both 19.
The two were kidnapped in the woods of southwestern Mississippi near Natchez.
Prosecutors said Seale, a former crop duster, was with a group of Klansmen when they abducted Moore and Dee from a rural stretch of highway in southwest Mississippi. The Klansmen took the teens into the woods and beat and interrogated them about rumors that blacks in the area were planning an armed uprising, prosecutors said.
The decomposed bodies were found in July 1964 as federal authorities searched for the bodies of three civil rights workers who had also disappeared that summer. That case became known as "Mississippi Burning" and overshadowed the deaths of Dee and Moore.
Thomas Moore, 68, of Colorado Springs, Colo., the brother of Charles Moore, told The Associated Press in a telephone interview that he took no joy in Seale's death.
"Rejoicing? That's not in my nature," Moore said. "All of that is behind me. I lived through the process. I hope he found peace with his god. My sympathies are with his family. I hope he found peace and I hope his family can pull together like mine has and get on with their lives."
Calls to Seale's defense attorney, Kathy Nester, now with the federal public defender's office in Salt Lake City, were not immediately returned Wednesday.
Seale and another man, Charles Marcus Edwards, briefly faced state murder charges in the deaths of Dee and Moore in 1964, but the charges were quickly thrown out. Prosecutors said the charges were dropped because local law enforcement officers were in collusion with the Klan.
Many people thought Seale was dead until 2005, when he was discovered living a town not far from where the teens were abducted. The case was reopened, and Edwards became the government's star witness after he was promised immunity from prosecution.
In March 2010, the 5th U.S. Circuit Court of Appeals ruled that the evidence against Seale was sufficient for the jury conviction in the trial that took place 43 years after the crimes. Later that year, the U.S. Supreme Court refused to hear Seale's appeal.