But the opening came as ISIS militants destroyed ancient statues in the Iraqi city of Mosul.
Museum officials said almost 15,000 pieces were looted in 2003, according to Agence France-Presse.
Officials have been able to recover 4,300 works, but are continuing efforts to track down the remaining antiquities.
“We are still tracking down more than 10,000 artifacts in markets and auctions. What we got back were the most important,” Qais Hussein Rashid, Iraq’s deputy tourism and antiquities minister, told AFP.
The extremist group released footage on Thursday showing supporters smashing ancient statues with sledgehammers because they deemed the works un-Islamic.
Mosul’s museums house many priceless artifacts from the Assyrian and Akkadian Empires.
The U.N.’s cultural body, UNESCO, welcomed the museum’s re-opening.
“The reopening of the Baghdad Museum is a powerful symbol, coming in the wake of the destruction perpetrated in Mosul,” UNESCO Director-General Irina Bokova said.
“To fight violent extremism and attacks against cultural heritage, we need more than ever to nurture the power of culture, supporting its fundamental role for dialogue and for social cohesion in Iraq and around the world,” she said.