Flanagan blazed the Gibson Course, setting a record time of 19 minutes, 36 seconds to win UNC's first ever individual national title in cross country.
The Marblehead, Mass., native won her second consecutive NCAA Cross Country Female Athlete of the Year award after winning the event.
"It's very exciting," Flanagan said.
"You pump up a national championship as one of those things that is so difficult to win, and this year it wasn't as hard as I expected it to be.
"That's a tribute to how hard I've worked and the mental and physical toughness I've gained over the last year," Flanagan said.
"It's a relief because it was expected of me to win it, especially after last year, but I was very confident going into the championship."
North Carolina's women's cross country team finished 21st at the NCAA Championship. Tar Heel coach Michael Whittlesey was pumped to see Flanagan's highly touted talent translate into a title.
"It was really exciting to see Shalane win the national title," Whittlesey said. "The pressure was taken off of her early when she trailed for the first mile, mile and a half, but then gained the lead and never relinquished it.
"Seeing her finish at the end was a great thrill."