Agency officials said that the trip would likely occur in the second week of March.
Condoleezza Rice, the US secretary of state, said that the US administration is very pleased about the invitation.
"We are really very pleased that the IAEA ... be able to go back into North Korea to be able to verify compliance with the agreement that is to take place over the next 60 days that would shut down the Pyongyang reactor and would seal it," Rice said during a visit to Ottawa.
Ban Ki-moon, the UN secretary-general, hailed the development as a "good beginning".
In a process that one UN official said "could take years", IAEA inspectors would be tasked with re-establishing monitoring of the plutonium-producing Yongbyon nuclear facility, and then being on site while it is closed and then dismantled.
The official said: "At the same time, there has to be some kind of declaration of what North Korea has and some way of following that up."
The US agreed to resolve financial restrictions it placed on a Macau bank - accused of complicity in counterfeiting and money laundering by North Korea - to pave the way for the disarmament-for-aid deal.
On Friday during a visit to Australia, Dick Cheney, the US vice president, expressed caution about the agreement, but called it a "first hopeful step".
The February 13 agreement signed by the two Koreas, the US, Japan, China and Russia specifies only that IAEA inspectors should be given the responsibility of supervising the closing of the Yongbon reactor.