Following his graduation, Flynn was a law clerk to Chief Judge Thomas Edward Fairchild of the United States Court of Appeals for the Seventh Circuit from 1975 until 1976.

[6] Flynn embraced a progressive platform as state chair and advocated to maintain Wisconsin's open presidential primary, a stance that put him at odds with the Democratic National Committee.

[7] During Flynn's first term as chairman, the state party reelected Senator William Proxmire and reclaimed the governorship after a four-year period of Republican control.

[9][10] In 1986, Flynn contested the Democratic nomination for the Senate seat held by Republican Bob Kasten, placing second to former deputy attorney general Ed Garvey in the primary.

Flynn has written two fiction novels since retirement, publishing a political satire called Pryme Knumber in 2012 and a followup work, Bernie Weber and the Riemann Hypothesis, in 2017.

Flynn has written a progressive political blog and was a regular pundit on the now-defunct Milwaukee television show Belling & Co, providing a Democratic perspective.

[14] The Republican Party of Wisconsin criticized Flynn for his past legal work on behalf of the Archdiocese of Milwaukee in cases involving allegations of sexual abuse.