Ames's novels include I Pass Like Night (1989), The Extra Man (1998), and 2004's Wake Up Sir!, described by The New York Times as "laugh-out-loud funny". In September 2008 Ames released The Alcoholic, his first foray into graphic novels. In 2009, he published a new collection of essays and fiction with Scribner, entitled The Double Life is Twice as Good.

While at the New York Press his columns were often recollections of his childhood neuroses and his unusual experiences, written in the gritty tradition of Charles Bukowski. These columns were collected in four nonfiction books, What's Not to Love?: The Adventures of a Mildly Perverted Young Writer (2000), My Less Than Secret Life (2002), and I Love You More than You Know (2006). Ames was also responsible for the Most Phallic Building contest which followed an article he wrote for Slate magazine where he claimed that the Williamsburg Bank Building in Brooklyn, New York, was the most phallic building in the world.

Ames became known as a raconteur in New York City following his 1999 one-man stage show, "Oedipussy," and continues to perform frequently with the New York based oral-storytelling performance company The Moth. He has also been a guest on The Late Show with David Letterman several times and played the lead role in the 2001 IFC film The Girl Under the Waves, an on-screen experiment in improvisational acting.

In 2004, Showtime commissioned Ames to develop a pilot based on his writings, titled What's Not to Love? Ames starred as himself, but it was not developed into a series, instead airing as a one time special in the winter of 2007-2008. Ames also appears in The Great Buck Howard, directed by Sean McGinly and starring John Malkovich, which debuted at Sundance in 2008.

Ames created the HBO series Bored to Death, which stars Jason Schwartzman as a struggling Brooklyn novelist named Jonathan Ames who moonlights as an unlicensed private detective. The show debuted on September 20, 2009.

The film adaptation of Ames's novel The Extra Man, starring Kevin Kline, John C. Reilly, Katie Holmes, and Paul Dano, was released in 2010.

Ames is a 1987 graduate of Princeton University and he holds a Master of Fine Arts in Fiction from Columbia University. He has been a visiting faculty member at Columbia University, The New School, and the Iowa Writers' Workshop.

Novels

• I Pass Like Night (1989)
• The Extra Man (1998)
• Wake Up Sir! (2004)

Essays

• What's Not to Love?: The Adventures of a Mildly Perverted Young Writer (2000)
• My Less Than Secret Life (2002)
• I Love You More Than You Know (2006)
• The Double Life Is Twice As Good: Essays and Fiction (2009)

Anthologies

• Sexual Metamorphosis: An Anthology of Transsexual Memoirs (2005)

Comics

• The Alcoholic, with Dean Haspiel (2008)

Television

• Bored to Death (Creator/Writer, 2009—Present)