The Yongbyon site processes spent fuel from power stations and has been the source of plutonium for North Korea's nuclear weapons programme.
The reactor was shut down in 2007 but Pyongyang said last year that it was operational again.
It has since conducted its fourth test of a nuclear weapon.
That and its multiple missile tests broke existing international sanctions and provoked further measures from the UN and individual countries.
The IAEA has no access to North Korea after being thrown out in 2009,  so relies largely on satellite data.
But the agency's head, Yukiya Amano, said recent images indicated "activities related to the five-megawatt reactor, expansion of enrichment facilities and activities related to reprocessing".
Vehicles have also been seen moving at the site and there are indications of warm water being discharged, which would suggest cooling operations.
Other North Korean observers have also said in recent months that the plant appears to be working again.
At North Korea's recent ruling party congress, leader Kim Jong-un reinforced his policy of economic development coupled with a strong nuclear programme.
North Korea appears to have restarted its nuclear facility at Yongbyon, the International Atomic Energy Agency (IAEA) has said.