The general, No Kwang Chol, returned Trump's offer of a handshake with a salute.
For its part, Beijing has broadly welcomed Trump's diplomacy with Kim.
USA presidents typically do not salute military officials with adversarial nations. In also expressing a desire to eventually remove the 28,500 American troops stationed on the peninsula, Mr Trump's shift could overturn longstanding USA policy in Asia and has received a cool reception from Australian Foreign Minister Julie Bishop.
White House press secretary Sarah Sanders said Mr Trump was just showing "common courtesy".
The move sparked a debate on whether the US President was out of line with his gesture.
North and South Korea on Thursday kicked off their first general-level military talks in over ten years at the truce village of Panmunjom, the Ministry of National Defense (MND) announced. "It was a awful thing, it was brutal, but a lot of people started to focus on what was going on, including North Korea". South Korea's presidential office has said it's trying to discern Trump's meaning and intent, but also that the allies should explore various ways to "further facilitate" dialogue with the North.
Republican Tim Walz tweeted the move wasn't something he would have done and described it as very bad. According to the Washington Post, North Korea's definition of "denuclearization" is different from Trump's.
"When you take over a country, a tough country, tough people and you take it over from your father - I don't care who you are, what you are, how much of an advantage you have - if you can do that at 27 years old, that's one in 10,000 that could do that", Trump said.More news: Domino’s Will Now Fix Your Potholes With ‘Paving For Pizza’ Program
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But Trump's move had always been suggested by China, and Beijing was quick to applaud its announcement on Wednesday.
Kim coming in from the global cold hasn't gone unnoticed by other world leaders with Vladimir Putin inviting Kim to the Kremlin.
Sergei Lavrov, the Russian foreign minister, was the first official from the Kremlin to meet with Kim when he travelled to Pyongyang in May.
Kim Yong Nam is the head of the presidium of North Korea's Supreme Assembly.
What was agreed at the summit?
Pompeo's comments Thursday come amid uncertainty over what the USA and North Korea's joint commitment "to work toward complete denuclearization of the Korean Peninsula" means in practice, and doubts over Trump's tweet that after the June 12 summit "there is no longer a nuclear threat from North Korea".
"I don't know exactly what form that will take, but I'm very confident that by some time in the next week or so we will begin the engagement", he said.
"North Korea still has all its nuclear missiles, and we only got a vague promise of future denuclearization from a regime that can't be trusted. Only then, there will be a relief from the sanctions".