He and first lady Melania observed a solemn moment of silence at the White House and later at the Pentagon.
Thousands are gathering nationwide to mark the deadliest attack on US soil.
Nearly 3,000 people died after hijackers crashed planes into New York's World Trade Center, the Pentagon and a rural Pennsylvania field in 2001.
Mr Trump and the first lady observed a moment of silence at the Pentagon at 09:37 (13:37 GMT), when US officials say American Airlines Flight 77 crashed into the building.