Trump and first lady Melania Trump listened as the names of the 184 people killed at the Pentagon that day were read aloud at the start of the ceremony.
Earlier, in a downpour at daybreak, Defence Secretary Pete Hegseth and top military officials stood outside and watched as a giant American flag was unfurled on the building struck by one of those planes a quarter of a century ago.
It is the second year in a row that Trump has marked the day at the Pentagon.
The president, who hails from New York, last attended the ground-zero ceremony there in 2024.
Vice President JD Vance is attending the New York observance alongside former presidents George W. Bush - who was in office on 9/11 - Bill Clinton, Barack Obama and Joe Biden.
Other administration officials are at a ceremony in Shanksville, Pennsylvania, where a fourth plane crashed in a field in the incident 25 years ago, after passengers and crew members stormed the cockpit and fought the hijackers.
At a Tuesday event at the Ellipse just outside the White House, Trump vowed to "never forget" victims, noting the September 11 attacks were one of few moments in history that "divide time into really what came before" and after.
That event, spearheaded by the Tunnel to Towers Foundation, showcased a massive, 6.4 metre, nearly 7700kg steel beam recovered from the South Tower of the World Trade Center in New York.
Travelling for months across the country as part of the Steel Across America tour, the beam was in New York for a procession on Friday retracing the steps of fallen New York City firefighter Stephen Siller.
On Wednesday, Trump issued a proclamation naming Friday as 'Patriot Day 2026', recounting the chronology of the 2001 day on which "the peace of our nation was shattered" and calling his administration "unwavering in its commitment to ensure that our nation is defended by the strongest and most lethal military the world has ever known".
The Republican mid-terms convention on Thursday night observed the 25th anniversary of the 9/11 attacks with families onstage in Dallas and firefighters in uniform as the song Ave Maria was played.
The names of the victims appeared on a screen and a bell was rung to commemorate the loss of firefighters.
Friday's milestone anniversary brings memorial rituals - wreath-laying, flag-flying, moments of silence, vigils and readings of victims' names - and volunteer projects in tribute to a day that about half of US adults remember as the most historic event of their lifetime, according to a new poll.
For others it's an occasion for private reflection - or, in many schools, education - about the attack that unfolded in a single morning but left nearly 3000 dead and a decades long trail of personal grief and far-flung wars.
