Flanagan won the 2017 Hyannis Half Marathon in Hyannis, Massachusetts running 1:14:38. Flanagan placed 11th at the 2017 Boston Marathon in 2:34:44 and 37th at 2017 World Championships in Athletics – Women's marathon in 2:39:47. In Fall 2017, Flanagan left Washington, D.C., Mizuno and Riadha Elite Development Program to join Boulder Track Club and Nike.