A source close to Yun said the decision to step away from his diplomatic post was the result of a combination of factors and was not intended as a protest statement.
Several sources familiar with Yun's decision told CNN he had planned to serve for only a year when the Trump administration took office and had already indicated a desire to retire for various personal and professional reasons.
But the source close to Yun added that he was certainly disappointed in what he viewed as a general lack of coherence on the administration's North Korea policy that made it difficult at times for him to discern the path forward.
The source described the administration's policy process as amateurish, but that was not the only reason for Yun's decision as he was a career diplomat familiar with messy policy making.
However, several State Department officials said they are disappointed by the timing of Yun's departure, given the urgent push to resolve tensions on the Korean Peninsula with diplomacy.iPhone transfer software
On Tuesday, State Department spokeswoman Heather Nauert thanked Yun for his many years of service following his decision to retire, but said the notion he's the only person who can handle the North Korea portfolio is "wrong."
"The State Department has 75,000 people that work for us around the world," she said, "and people like Acting Assistant Secretary Susan Thornton and Chargé D'Affaires Marc Knapper are among those who can pick up the slack." The administration's policy on North Korea, she noted, hasn't changed.
The White House also declined to provide an estimate for when President Donald Trump might name an ambassador to South Korea -- only fueling uncertainty surrounding the administration's approach.
"I don't have a timeline and I don't have any personnel announcements on that position specifically," press secretary Sarah Sanders said.
The US has been without a permanent ambassador to Seoul since Trump assumed office with the position filled by the chargé d'affaires.
"Today's announcement that Ambassador Joe Yun, our top North Korea diplomat, is resigning is yet another setback in the Trump Administration's chaotic and uneven approach to diplomacy in the Korean peninsula and to the overall institutional integrity of the State Department," said Democratic Sen. Bob Menendez of New Jersey, the ranking member of the Senate Foreign Relations Committee.
"President Trump has made clear his fundamental misunderstanding of the role of diplomacy, and his disdain for the men and women of the State Department who have dedicated their lives to pursuing the foreign policy interests of the United States," he said in a statement.
Yun's retirement is also raising concerns about deepening divisions within different parts of the administration over how best to proceed on the issue despite hopes for diplomatic progress following the Olympics in South Korea.
"What we've seen in recent months is an unraveling of what was once a fairly coherent North Korea policy," according to CNN military analyst John Kirby, who added that internal issues have created a divide with the State Department and Pentagon on one side and the National Security Council on another.
"Some experts believe national security adviser H.R. McMaster has been running the National Security Council as its own competitive agency rather than serving in its traditional convening capacity -- and that has caused a rift with other branches of the administration and a disconnect in the overall strategy," Kirby said.
While Tillerson and Defense Secretary James Mattis have consistently said the US should exhaust all diplomatic options before considering the use of military force, the loss of key diplomatic voices like that of Yun could precipitate a more hawkish consensus within the White House, Kirby added.
And some worry that Yun's retirement puts the US at risk of being left out of the negotiating process.
"Now, with one less voice for forward-leaning diplomacy both inside the administration and in the region, the United States further risks being missing in action when it comes to advancing a