Han Tak Lee, 79, who was being held in a state prison in Pennsylvania, was to appear in federal court in Harrisburg later Friday, his lawyer said. A magistrate was expected to set bail conditions.
The Monroe County district attorney in New York has a Dec. 6 deadline to decide whether to prosecute Lee again.
U.S. District Judge William Nealon dismissed Lee's conviction Aug. 8. Nealon said new research has determined the evidence used to show the fire that killed Ji Yun Lee was deliberately set is not proof of arson.
"The verdict in the matter rests almost entirely upon scientific pillars which have now eroded," U.S. Magistrate Judge Martin Carlson wrote in a June report to Nealon.
Lee, who owned a clothing store in New York, brought his daughter to Camp Hebron in Stroud, N.Y., in 1989, after she became violent and began throwing things in his family's New York City apartment. They were staying in a cabin that caught fire that night.
Firefighters found Lee sitting outside with his luggage, while his daughter's body was inside. He said he had gone inside after first escaping the flames to try to find her.
An autopsy determined Jun Yi died from burning and also found marks on her necks, suggesting she might have been strangled.
John J. Lentini, an expert on fire investigation who re-examined the evidence, said that prosecutors used evidence like pour patterns and crazed glass that were believed at the time to be evidence of arson. But new research has shown they can occur in fires that are not deliberately set.
Carlson found that the rest of the state's case consisted of "thin and equivocal reeds" of evidence.
A number of arson convictions in recent years have been discredited.
In one of the most notorious cases, Cameron Todd Willingham was executed in Texas in 2004 for setting a fire that killed his three young daughters, although one expert reported a few weeks earlier that there was no reliable evidence of arson. The execution remains controversial with charges that Gov. Rick Perry, who signed Willingham's death warrant, interfered with an investigation by the Texas Forensic Science Commission.