Flight 93 was hijacked on that day in 2001, and the newly-dedicated Tower of Voices now stands in the field where the aircraft crashed.
The 9/11 plane strikes, which destroyed the Twin Towers and left a gaping hole in the Pentagon, killed almost 3,000 people, majority in Manhattan.
The terror attacks were the deadliest in the United States history, killing 2,996 people.
Hundreds of people, including survivors and families of the victims, gathered and remembered those who died by reading out every name.
US marks 17th anniversary of the 9/11 attacks
Trump and his wife, Melania, traveled to the Flight 93 National Memorial from Washington and paused for a moment of reflection while overlooking the field where the plane crashed.
Trump observed the solemn anniversary for the first time as president a year ago.
In all, four planes were hijacked by Al-Qaeda militants who used them to topple the trade center's twin towers and hit the Pentagon.
The tower now holds eight wind chimes, but will eventually hold 40, one for each traveler and crew member on the plane. It's where a California-bound commercial airliner crashed on september 11, 2001, after the 40 passengers and crew members learned what was happening and attempted to regain control of the aircraft.
Mr Trump is the third sitting president to attend the crash site, 70 miles (110km) southeast of Pittsburgh. "And I watched in Jersey City, New Jersey, where thousands and thousands of people were cheering as that building was coming down", Trump said at the time. The annual 9/11 commemorations are by now familiar rituals, centered on reading the names of the dead. Another sister, Chaundera, had an answer for anyone who wonders why families still come to such ceremonies after 17 years. But each year at ground zero, victims' relatives infuse the ceremony with personal messages of remembrance, inspiration and concern. In June, doors opened at the 80-story 3 World Trade Center, one of several rebuilt office towers that have been constructed or planned at the site.More news: Apple iPhone XS, iPhone XC, MacBook, iPad Pro price and specs leaked