The unusual trip by Jeffrey Feltman, which runs to Friday, comes less than a week after North Korea said it test-fired a new ballistic missile capable of reaching the United States.
AFP journalists saw Feltman arrive in a UN-flagged car at the Chinese capital's international airport in the morning. North Korea's Air Koryo airline has a 0455 GMT flight to Pyongyang today.
His trip comes a day after the United States and South Korea launched their biggest-ever joint air exercise - manoeuvres slammed by Pyongyang as an "all-out provocation".
Feltman arrived in China yesterday as Beijing is one of the few transit points to North Korea in the world.
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China is Pyongyang's sole major diplomatic and military ally, and its main trade partner.
Once in the North, Feltman will discuss "issues of mutual interest and concern" with officials, UN spokesman Stephane Dujarric said, adding he was unable to say whether Feltman will meet with the reclusive state's leader Kim Jong-Un.
It will be Feltman's first visit to North Korea since he took office five years ago, and the first by a UN under- secretary-general in more than seven years.
The UN Security Council has hit the isolated and impoverished North with a package of sanctions over its increasingly powerful missile and nuclear tests, which have rattled Washington and its regional allies South Korea and Japan.
Pyongyang ramped up already high tensions on the Korean Peninsula five days ago when it announced it had successfully test-fired a new ICBM, which it says brings the whole of the continental United States within range.
Analysts say it is unclear whether the missile survived re-entry into the earth's atmosphere or could successfully deliver a warhead to its target - key technological hurdles for Pyongyang.
In a separate message to staff, Cathay general manager Mark Hoey said the crew described seeing the missile "blow up and fall apart," The South China Morning Post reported.
In recent years, Pyongyang has accelerated its drive to bring together nuclear and missile technology capable of threatening the US, which it accuses of hostility.
US President Donald Trump has engaged in months of tit- for-tat rhetoric with Kim, pejoratively dubbing him "Little Rocket Man" and a "sick puppy".
Over the weekend, Pyongyang countered that Washington was "begging for nuclear war" as the North blasted the joint US- South Korean drills.
As well as featuring the latest generation of stealth fighters, this year's war games involve simulated precision attacks on the North's military installations, including its missile launch sites and artillery units, Yonhap news agency said, citing unnamed Seoul sources.
As tensions surged, US Senator Lindsey Graham, an influential Republican and foreign policy hawk, warned that the US was moving closer to "preemptive war" if the North continued its nuclear tests.
But some Trump advisers say US military options are limited when Pyongyang could launch an artillery barrage on the South Korean capital - only around 50 kilometers (30 miles) from the heavily-fortified border and home to 10 million people.
Tokyo's parliament yesterday slammed the North's weapons programme as an "imminent threat". Last week's missile landed in Japan's economic waters.
China's foreign ministry warned that the situation on the Korean peninsula remained "highly sensitive" and called on all sides to "do more things to ease the tension and avoid provoking each other."
While analysts agree the latest test showed a big improvement in potential range, they say the North may not have yet mastered all the technology required to successfully hit the US with a nuclear warhead.