It was unclear whether Mr. Trump raised human rights violations in the country, despite calls for him to do so.
The previous US administration had spoken out against Mr. Duterte’s war on drugs, which has killed almost 4,000 people.
Mr. Trump is almost at the end of an extensive Asia tour.
The first meeting between the two took place at the Association of South-East Asian Nations Summit
It was closely watched as both men are known for striking a controversially outspoken and direct tone.
After the private meeting, the US President did not respond to questions about whether he had raised the subject of human rights while a spokesman for Mr. Duterte said the topic had not been discussed.
White House spokeswoman Sarah Sanders later said the topic was mentioned briefly in their private meeting, in the context of the war on drugs, but did not give further details.