This marks the first time a European leader has met with the president since the start of the trade conflict.
The U.S. president has struck back against U.S. allies with tough tariffs and is planning to impose stringent trade penalties on China later this week.
In a paper released this week, the European Commission said Trump's tariffs would be "self-defeating and would weaken the U.S. economy".
The E.U. has since retaliated by threatening the US with potential auto tariffs with its own further counter measures worth up to $300 billion.
Asked if he planned to pull out of the WTO, Mr Trump said the trade organisation had treated the USA "very badly, and I hope they change their ways".
"If we do work it out, that'll be positive, and if we don't, it'll be positive also, because..." said Trump.
"Just think about those cars that pour in here", Trump continued. Trump responded with reference to his auto tariff. She and Prime Minister Rutte discussed the importance of ensuring that trade between the Netherlands and the United Kingdom remained as frictionless as possible following the UK's exit from the EU.
"It's not positive", finished Rutte. That will be good, and if we do work it out, that'll be positive, and if we don't, it'll be positive also.
CBS News White House correspondent Mark Knoller said the Dutch leader was "clearly in disbelief at the lack of decorum".
"We are allies", pushed Rutte.
In May, Trump commissioned an investigation by the Commerce Department into the state of automobile imports into the US, prompting European Union leaders to send Trump an 11-page document last Friday (June 29) threatening to levy taxes on $290 billion in USA goods.
"Is it always like this?" the Dutch leader asked Mr. Trump with a laugh.