The Yongbyon plant, about 100km north of the capital Pyongyang, is home to the North's sole plutonium producing reactor.
The plant was the focus of North Korea's efforts to produce a nuclear weapon that culminated in the country's first-ever test explosion in October last year.
During his stay in the North Hill is also expected to hold talks with his North Korean counterpart ahead of a fresh round of six-nation talks in Beijing later this month.
Before travelling to the North on Monday Hill said he would also be discussing a full inventory of all the North's nuclear programmes.
The disclosure of all North Korea's nuclear weapons programmes is a key component of a six-nation aid for disarmament deal agreed in Beijing earlier this year.
Hill last visited North Korea in June and was at that time the first senior US official to do so in more than four years.
The disarmament deal is being touted by the Bush administration as a foreign policy success, but many critics have accused the US president of taking too weak a line with North Korea in order to distract attention from failing policies in Iraq.