Flanagan turned back a challenge from Olympian Kim Conley to win the 8k women's race going away in 25 minutes, 49 seconds. Teammate Emily Infeld was fourth in 26:47.7.
Flanagan broke contact at about the six-kilometer mark.
"I was hoping to shake her a little earlier," Flanagan said in a postrace interview with RunnerSpace.com. "She hung tough. That made it more fun. She made it a battle for so long."
The top six finishers qualified for the U.S. team for the World Cross Country Championships, although Flanagan said after the race she would forgo the world meet to train for the Boston Marathon.