It will leave another gaping hole in the United States' staffing on Korean issues.
His departure comes amid glimmers of hope for a diplomatic opening between Pyongyang and Washington. In January sources told CNN the long-rumored candidate, Victor Cha, would no longer be nominated.
"The Secretary has reluctantly accepted his decision and wished him well", State Department spokesperson Heather Nauert said in a statement provided to HuffPost.
Yun, who also serves as the US top negotiator for the now defunct six-party talks to denuclearize the North, traveled to Pyongyang last June to help secure the release of the late Otto Warmbier, an American student who had been detained there and died shortly after his release.
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Warmbier returned to the United States with significant brain damage and died just days later.
Yun's abrupt departure, coupled with Cha's rejection, highlights an alarming lack of Korea expertise in the Trump administration, at a crucial time when seasoned voices are particularly needed. That was the last time the three men have been seen or heard from.
Yun traveled to North Korea last year to retrieve Otto Warmbier, the American student who had been detained for over a year. The former North Korean intelligence chief was thought to have organized attacks on South Korean territory and naval vessels. Yun has been regularly meeting with his counterpart there, Pak Song Il.
In this February 29, 2016, photo, American student Otto Warmbier cries while speaking to reporters in Pyongyang, North Korea. Since the inauguration in January a year ago, the Trump administration took toughest ever stance on North Korea, demanding de-nuclearization.
The South Korean-born Yun has led the U.S. outreach to North Korea, quietly pursuing direct diplomacy, since taking his post under former U.S. President Barack Obama in 2016.
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But the signals have been mixed, to say the least.
North Korean diplomats often spar with USA officials at the disarmament body in Geneva. This, too, keeps Tokyo's position consistent with that of Washington, which rolled out new unilateral sanctions on Pyongyang on Friday. Kang also told the UN-backed Conference on Disarmament that sanctions are "not meant to bring down North Korea", but to convince it to join other nations in working towards denuclearization.
"Ambassador Yun has served with distinction for more than 30 years. we are sorry to see him retire".
And former deputy assistant secretary of defence for East Asia Abraham Denmark said on Twitter that Mr Yun's retirement was "a huge loss for the U.S. government at a critical moment".
"Joe Yun is the only senior official left at State who has experience dealing with the complexities of North Korea policy".
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He met with leader Aung San Suu Kyi and found her resisting calls for an worldwide investigation. Satellite imagery reviewed by Human Rights Watch suggests that the demolitions are ongoing.