On January 14, 2012, Flanagan won the U.S. Olympic Trials Marathon in Houston, setting the event record at 2:25:38. She moved on to represent Team USA at the Olympic women's marathon in London, finishing 10th with a time of 2:25:51. She defeated a high class field at the Lisbon Half Marathon in March, recording a time of 1:08:52. She came in 25th at the 2012 IAAF World Half Marathon Championships.