Hill said his main aim was to persuade the North to accept a system to verify statements made about its nuclear programme, and to answer US suspicions of a secret project to enrich uranium for weapons.
Earlier this week the US envoy said that negotiations with the North had reached a "very tough" phase.
"What they have been doing, obviously, goes against the spirit of what we have been trying to accomplish," he told reporters on Tuesday night after talks with Kim Sook, his South Korean counterpart.
Hill said the two sides had held some discussions through North Korea's UN mission in New York and "we thought it would be useful to try to have those discussions in Pyongyang".
North Korea, which tested an atomic weapon in October 2006, began disabling its ageing reactor and other facilities at Yongbyon last November under a pact with South Korea, China, Japan, Russia and the United States.
But it announced last month that it had halted work in protest against Washington's refusal to drop it from its blacklist of alleged state sponsors of terrorism, as promised under the deal.
Washington says the North must first accept strict outside verification of the nuclear inventory that Pyongyang handed over in June.
North Korea says verification is not part of this stage of the agreement and accuses the US of violating its dignity by seeking "house searches" as in Iraq.