He was born and grew up in Scituate, Massachusetts, south of Boston. His parents divorced when he was young and his mother committed suicide when he was 22. He drifted through several jobs before starting work at a homeless shelter in Boston, where at age twenty-seven, he met his estranged, homeless father for the first time. Flynn earned an Master of Fine Arts in creative writing from New York University and teaches part-time at the University of Houston Creative Writing Program. He used to teach at Columbia University, where he was a poet and educator. His long-time partner is actress Lili Taylor, with whom he shares a home in New York.

Flynn's works have appeared in New American Poets: A Bread Loaf Anthology, American Poetry: The Next Generation, The New Yorker, The Nation, Fence, The New York Times, and The Paris Review.

Poetry collections

• Some Ether: Poems (Graywolf Press, 2000)
• Blind Huber: Poems (Graywolf Press, 2002)

Memoir

• Another Bullshit Night in Suck City: A Memoir (W. W. Norton & Company, 2004)
• The Ticking Is the Bomb: A Memoir (W.W. Norton, 2010)

Textbooks

• A Note Slipped Under the Door: Teaching from Poems We Love (Stenhouse Publishers, 2000, co-authored with Shirley McPhillips)

Plays

• Alice Invents a Little Game and Alice Always Wins: A Play (Faber & Faber, 2008)

Miscellaneous

• Crossroads (2001), with Josh Neufeld