In 2015, Flanagan was elected to fill a vacancy in the Minnesota House, representing a section of Minneapolis's western inner-ring suburbs.

The daughter of American Indian land rights and sovereignty activist Marvin Manypenny,[5] Flanagan was raised by a single mother, a phlebotomist, in St. Louis Park, Minnesota.

[9] Flanagan received a bachelor's degree in child psychology and American Indian studies from the University of Minnesota in 2002.

[8] In 2008, she challenged incumbent Minnesota Representative Joe Mullery in the Democratic primary, but dropped out of the race due to her mother's health problems.

[14] As executive director of Children's Defense Fund-Minnesota, she also advocated for the successful 2014 effort to raise Minnesota's minimum wage.

[6] In 2016, she began training for The Management Center, helping social justice leaders build and run effective, equitable, and sustainable organizations.

[16] Susan Allen (Rosebud) and Republican Steve Green (White Earth Ojibwe) were the only other Natives in the Minnesota State House at that time.

Three other Native women sought election to the Minnesota legislature in November 2016: Mary Kelly Kunesh-Podein (Standing Rock Lakota) and Jamie Becker-Finn (Leech Lake Band of Ojibwe) ran for state representative seats and Chilah Brown (Mille Lacs Band of Ojibwe) ran for the Minnesota Senate.

[18][17] In 2017, Flanagan became a candidate for lieutenant governor, joining U.S. Representative Tim Walz, who won the DFL primary in the 2018 Minnesota gubernatorial election.

Later, she sponsored a mandate for tribal consultation in state affairs[23] and as lieutenant governor created the nation's first Missing and Murdered Indigenous Relatives Office.

[29] On January 12, 2018, Flanagan announced on her personal Facebook page that she was in a relationship with the Minnesota Public Radio News host Tom Weber; MPR News announced that day that it was reassigning Weber to no longer cover "the governor's race, the Legislature, potential legislation, public policy involving the executive or legislative branches or any topic related to the November 2018 election.