Mohammed Soltan, the son of a prominent member of the now-outlawed Muslim Brotherhood, was arrested in August 2013 when security forces came looking for his father at his home.
His family said they didn't find the father at the time, but arrested him instead. His father, Salah, was detained later.
Soltan, a 27-year-old Ohio State University graduate and former Barack Obama campaigner, had been on a hunger strike over his detention of more than 14 months and his family said his health had been rapidly deteriorating.
In a statement, Soltan's family thanked those who helped work for his release, saying that the US government had secured his deportation back home after extensive efforts.
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"After spending several hundred days on hunger strike, and many months in solitary confinement, Mohammed's health is dire," his family said.
"He will receive medical treatment as soon as he arrives on US soil and will spend the immediate future with his family recovering."
The case is rooted in the violence that swept Egypt after the military-led ouster in July 2013 of Islamist President Mohammed Morsi, a veteran Brotherhood leader.
His supporters set up protest camps in Cairo. Security forces violently dispersed the sit-ins in August 2013, killing hundreds. In retaliation, many police stations and churches came under attack.
President Abdel-Fattah el-Sissi, who as army chief overthrew Morsi amid mass protests against the Islamist leader, issued a decree in November that allows him to deport foreign defendants convicted or accused of crimes.