The university has been doing this every year for over a decade now.
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Each flag represents a life lost on that day in 2001. The Waves of Flags display includes American flags as well as flags of other countries who lost citizens in the attack.
The display will remain in place until Sept. 21.
MORE: 9/11 timeline - How the September 11 attacks unfolded
9/11 Timeline: How the September 11 attacks unfolded
A private ceremony was planned in front of the flags display on Monday. The event, which was set to include remarks from actor Chris Pratt, is closed to the public. However, the public is invited to visit and is welcome to leave a note or prayer attached to any flagpole at the Waves of Flags display.
The annual display aims to educate and commemorate that tragic day.
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"Today we're here to remember and to spend this time to reflect and also to be unified, and that's an important part of this day, is to come in unity. The idea is for individuals to walk through and just to reflect and spend this time to look at each and every flag that represents somebody," said Michael Friel, the director of communications at Pepperdine University.
This is one of many remembrance ceremonies that took place across Southern California on Monday.
At the L.A. Fire Department Memorial Training Center, Mayor Karen Bass rang 10 bells in honor of those who lost their lives. Long Beach also held a Last Alarm Tribute at Fire Station 1, followed by a wreath-placement and moment of silence. Ceremonies were also held at all five Santa Monica fire department stations.
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