On June 26, 2016, Flanagan set an American record and won the road Boston Athletic Association 10K in Boston in 30:52. She lowered her national record by 11 seconds and beat the previous B.A.A. 10K event record by 12 seconds (31:04, held by Mamitu Daska since 2014). On August 14, 2016, Flanagan placed 6th at the 2016 Summer Olympics women's marathon in 2:25:26.