An IAEA statement also confirmed on Thursday that Pyongyang had stopped "disablement work", a move North Korea had threatened in light of the US's delay in removing it from the "terror" list.
The North says it will reactivate Yongbyon's plutonioum-reprocessing plant, and other facilities at its main nuclear site.
North Korea had banned IAEA inspectors from the reprocessing plant last month after demanding they remove agency seals from the facility. But the inspectors continued to have access to the rest of the site until Thursday.
Access denied
"Since it is preparing to restart the facilities at Yongbyon, the DPRK [Democratic People's Republic of Korea] has informed the IAEA that our monitoring activities would no longer be appropriate," the UN nuclear watchdog said.
It said the North "informed IAEA inspectors that effective immediately, access to facilities at Yongbyon would no longer be permitted" and "also stated that it has stopped its [nuclear] disablement work".
The IAEA said its inspection team would remain on the site until told otherwise by the authorities.
The US state department said it does not view North Korea's statement as the end of a six-nation agreement on ending North Korea's nuclear programme.
"This is a regrettable step, but one that is reversible," Sean McCormack, the state department spokesman, said.
Conditions remain
The delisting depends on North Korea agreeing to a plan to verify an account of its nuclear activity that it submitted over the summer, US diplomats have said.
North Korea would be put back on the list if it does not comply with the plan and abandon nuclear arms, they said.
Pyongyang had disabled its Yongbyon nuclear facility under the initial phases of the deal, but since August has been reversing that because the US has not removed it from the list as agreed in the deal after North Korea provided a declaration of its nuclear programme in June.
The US has said it will fulfil the obligation only when North Korea accepts a plan to verify is disablement.
But while Christopher Hill, the chief nuclear negotiator, was in North Korea, he proposed a face-saving compromise under which the North would be provisionally removed from the list as soon as it deposits with China an agreement on verification, according to US officials.