"We are going directly to the nuclear site at Yongbyon," Adel Tolba, the leader of the 10-man International Atomic Energy Agency team, said on Saturday.
"We will resume our work when we arrive."
North Korea has not said when the shutdown, which is part of disarmament agreement reached in February, will be completed..
But Christopher Hill, US nuclear envoy, said it would happen in days.
"I think it's a matter of today, tomorrow, maybe Monday," he said during a visit to Japan."Fuel oil shipment
"North Korea has only one card in hand and that is its nuclear programme
Rahy, Tehran, Iran
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Pyongyang will receive 50,000 tonnes of heavy fuel oil for closing the facility and that will rise to one million tonnes once the whole nuclear programme is dismantled.
Saturday's visit will be the first time since 2002 that IAEA inspectors have been allowed to inspect the reactor.
Tolba said that his team would stay in North Korea as long as was needed to complete the work.
The Soviet-era Yongbyon facility, which produces raw material for bomb-making plutonium, is at the heart of the North's nuclear programme which culminated in its first atomic weapons test last October.
The two Koreas, the US, China, Russia and Japan will resume talks on Wednesday next week to discuss how Pyongyang proceeds towards full denuclearisation.
Hill also said he expected the North to submit a list of its nuclear facilities within months, as was agreed upon in February's round of talks.
"We expect the comprehensive list in a matter of several weeks, possibly several months," he said.
Hill also stressed that the shutdown of Yongbyon was only the first step.
"I also don't want people to think this shutdown is the biggest and only event."