Danny Fenster's release follows "face-to-face" talks between a former US diplomat and junta chief Min Aung Hlaing.
Myanmar has released an American journalist who had been imprisoned since May.
Danny Fenster was deported on the same day of his release on Monday, a day before he was due to face terror and sedition charges that could have jailed him for life.
The 37-year-old's release was secured following "face-to-face negotiations" between former top US diplomat Bill Richardson and junta chief Min Aung Hlaing, Richardson's organisation said in a statement.
Fenster would travel home to the US "through Qatar, over the next day and a half," the Richardson Center said, adding it was looking forward to reuniting Danny with his parents and brother.
A photo posted by the Richardson Center showed Fenster, looking thin and gaunt, standing in shorts and flips flops in front of a small plane alongside the former New Mexico Governor on the tarmac in Myanmar's capital Naypyidaw.
Junta spokesperson Zaw Min Tun confirmed he had been freed and would be deported from the country.
Fenster had been working at local magazine Frontier Myanmar for around a year and was arrested as he headed home to see his family in May.
He was jailed for 11 years last week for incitement, unlawful association and breaching visa rules and had been due to appear in court on Tuesday to face sedition and terror charges – which could have seen him jailed for life.
Crackdown on press
Myanmar has been in turmoil since the military seized power in a February coup and ousted Aung San Suu Kyi's elected civilian government.
The military has squeezed the press since taking power in a February coup, arresting dozens of journalists critical of its crackdown on dissent, which has killed more than 1,200 people according to a local monitoring group.
The junta has tried to tighten control over the flow of information, throttling internet access and revoking the licences of local media outlets.
More than 100 journalists have been arrested since the putsch, according to Reporting ASEAN, a monitoring group.
It has said at least 30 are still in detention.