Ledecky won the 800 in 8:18.47 in the finals of the Phillips 66 National Championships at the William Woollett Jr., Aquatic Center in Irvine on Wednesday, nearly six seconds faster than the second-place swimmer.
She set the world record about six weeks ago with an 8:11.00 at a meet in Texas.
"I know that there's a great history there, and I'm really excited about my decision," Ledecky said. "I'm looking forward to swimming for Stanford and competing at the NCAA level there."
Stanford grad Maya DiRado missed qualifying for the championship final of the 200-meter butterfly by 1/10th of a second.
She was given a reprieve when Olympian Elizabeth Beisel withdrew and DiRado took full advantage of the situation and swam two seconds faster than her qualifying time to finish fourth in 2:09.76. Cammille Adams won the race in 2:08.06.
Incoming Cardinal freshman Simone Manuel could not hold off the late charge from Olympic gold medalist Missy Franklin, who came from third place to win the 100 free in 53.43, .07 seconds off her lifetime best.
"I absolutely have her to thank for that," Franklin said. "I love racing against her. She goes out like a bullet and that's where I need to work. Having her there in the second half, having to dig down deep, was awesome."
Manuel, who led Olympic gold medalist Natalie Coughlin by .17 seconds halfway through the race, finished second in 53.66 after going 53.60 in the prelims.
Stanford sophomore and Olympian Lia Neal placed fifth in 54.47. Coughlin finished seventh in 54.52.
Manuel swam the sixth-fastest time in the world this season for the top qualifying time (53.60) in the morning prelims.
Stanford had three swimmers in the 'B' final of the 100 free, with senior Maddy Schaefer leading the way at 54.96, good for third in the heat and 11th overall. Grad Felicia Lee's 55.10 and grad Andi Murez, who came in at 55.16, immediately followed her.
On the men's side, Cardinal grad Bobby Bollier finished sixth in the 200 fly with a time of 1:57.95. Cal's Tom Shields won the event in 1:55.09.
The Stanford 400 free relay team of Thomas Stephens, Drew Cosgarea, Jeff Garnier and Sean Duggan finished second in a close race with Swim Mac. Stanford finished at 3:21.38, .07 seconds behind the winners.
The event serves as the U.S. National Team selection for the 2014 Pan Pacific Championships, 2014 Jr. Pan Pacific Championships, 2015 World Championships, 2015 World University Games, and 2015 Pan American Games.
Overall, six past, present and future Stanford swimmers finished among the top 17 in the morning preliminaries.
The meet continues through Sunday.