According to Secretary of State Rex Tillerson, the 22-year-old student was on his way home to the US.
Otto Warmbier’s family told media they had found out only last week that their son has been in a coma since shortly after his trial in March 2016.
He was sentenced to 15 years of hard labor for attempting to steal a propaganda sign from a hotel.
Otto Warmbier is an economics student from the University of Virginia, originally from Cincinnati, Ohio.
He was in North Korea as a tourist with Young Pioneer Tours when he was arrested on January 2, 2016.
Otto Warmbier appeared emotional at a news conference a month later, in which he tearfully confessed to trying to take the sign as a “trophy” for a US church, adding “the aim of my task was to harm the motivation and work ethic of the Korean people”.
Foreign detainees in North Korea have previously recanted confessions, saying they were made under pressure.
After a short trial on March 2016, Otto Warmbier was given a 15-year prison sentence for crimes against the state.
His parents Fred and Cindy told CNN in early May that they had had no contact with their son for more than a year.
In a statement, Fred and Cindy Warmbier said: “Otto has left North Korea. He is on a Medivac flight on his way home.
“Sadly, he is in a coma and we have been told he has been in that condition since March 2016. We learned of this only one week ago.”
They were quoted by the Washington Post as saying they had been told their son had contracted botulism, a rare illness that causes paralysis, soon after his trial in March 2016.
Otto Warmbier was given a sleeping pill and had been in a coma ever since, the newspaper said.
Rex Tillerson made no mention of Otto Warmbier’s condition in his statement, saying only that he was on his way home to be reunited with his family and would not make any further comment, out of respect for the privacy of the family.
The US has in the past accused North Korea of detaining its citizens to use them as pawns in negotiations over its nuclear weapons program.
The arrests have come at a time of heightened tension between North Korea and the US and its regional neighbors.
Otto Warmbier’s release comes hours after former NBA star Dennis Rodman arrived in North Korea.
Dennis Rodman is a friend of North Korean leader Kim Jong-un and has made several visits to the country in recent years.
There was some speculation that Dennis Rodman might plead the case for the American detainees, but en route to North Korea the basketball star told reporters “my purpose is to actually see if I can keep bringing sports to North Korea”.
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