Flanagan was one of three Tar Heels in the top 10 and led North Carolina to a second-place finish with 55 points behind N.C. State's 39 points.
Matt Weiss' 23rd-place finish led the North Carolina men's team, which finished eighth with 221 points. Weiss finished in 25 minutes, 21.2 seconds.
N.C. State won the men's event, as well, with 26 points, and Wake Forest's Nathan Sisco was the individual champion in 24:23.5.
Flanagan ran a 20:34.3 race on the 6,000-meters course in taking her second title. Teammate Carol Henry finished eighth in 21:34.2 and was named Freshman of the Year.
Henry was followed by Tar Heel Kim Timberlake in ninth at 21:34.9. Flanagan, Henry and Timberlake were each named to the ACC All-Conference Team.
