The 62-year-old Egyptian diplomat received the unanimous support of the 35-member board after some objections on procedural grounds by the Japanese.
The United States had indicated it was prepared to support Mr. ElBaradei, but is still hoping for a tougher policy on Iran.
Mr. ElBaradei has always favored continued inspections and work in Iran instead of sending the file to the U.N. Security Council for possible sanctions, supported by Washington.
The United States believes there is plenty of evidence to show that Iran is working on a secret nuclear-weapons program, something strongly denied by Tehran.
Mr. ElBaradei is not convinced there is sufficient proof of a weapons program, although he has often reprimanded Iran for its failure to co-operate with the agency and for breaching its international treaty obligations.
The board will hear a new report on Iran later this week that is expected once again to show that Iran is dragging its feet in coming clean on a nuclear program that was kept secret from the world for almost two decades.
Editor Rebecca Johnson, of the Acronym Institute's journal "Disarmament Diplomacy", says it is unlikely that the matter will be referred to the U.N. Security Council as Mr. ElBaradei's position is now stronger.
"It strengthens his hand and I would also say its part of realpolitik recognition by the United States that the U.S. is not the best to deal with the situation and that they have to work with and actively support and stop undermining not only Dr. ElBaradei but of course also the EU three," she said.
France, Germany and Britain are currently negotiating with Iran offering nuclear technology in return for a promise by Tehran that it will give up its enrichment program. Details of a package deal are expected at the end of July.