At the World Cross Country Championships on March 20, 2011, Flanagan improved on her 12th place from the year before to place third, with a time of 25:10. She led the Team USA squad to a bronze medal. Flanagan was the first non-African born medalist in the event since 2004. She competed in the June 2011 USA Championships in the 10,000 m and won with a time of 30:59.57, qualifying her for the 10,000 m at the World Championships.