"Obviously, we are all heartbroken," Obama said after signing the condolence book in the embassy's entrance hall.
The president expressed US "solidarity with the people of the Netherlands" and offered "deepest condolences" on behalf of the nation.
One dual US-Dutch national was among the 298 people killed on Malaysia Airlines Flight 17, which was downed over rebel-held east Ukraine. More than half of the victims were Dutch.
Obama said Washington would work with the Netherlands "to make sure their loved ones are recovered and justice" is done.
