Pinkwater tends to write books about social misfits who find themselves in bizarre situations, such as searching for a floating island populated by human-sized intelligent lizards (Lizard Music), exploring other universes with an obscure relative (Borgel), and discovering that their teeth can function as interstellar radio antennae (Fat Men from Space). They are often, though not always, set in thinly...or not at all...disguised versions of Chicago and Hoboken, New Jersey. He often includes Chicago landmarks and folkloric figures from his childhood in 1950's Chicago, regardless of when the book is set. An example of this is the recurring character the Chicken Man, a mysterious but dignified black man who carries a performing chicken on his head. This character is based on a shadowy figure from 1950's Chicago; after Pinkwater made him a lead character in Lizard Music he received letters from Chicago residents who remembered the Chicken Man. Pinkwater also pays tribute to the Clark (a movie theatre on Clark Street), Bughouse Square, and Ed & Fred's Red Hots. Another common theme is Jewish culture, with many characters speaking in Yiddish-influenced dialogue or participating in Borsht Belt culture (Wempires).

In 1995, Pinkwater published his first adult novel, The Afterlife Diet, in which a mediocre editor, upon dying, finds himself in a tacky Catskills resort populated by "circumferentially challenged" deceased.

Pinkwater authored the newspaper comic strip Norb, which was illustrated by Tony Auth. The strip, syndicated by King Features, was cancelled after 52 weeks.

Pinkwater is also a longtime commentator on National Public Radio. He regularly reviews children's books on NPR's Weekend Edition Saturday. For several years, he had his own NPR show, Chinwag Theater. Pinkwater is also known to avid fans of the NPR radio show Car Talk, where he has appeared as a (seemingly) random caller, commenting, for example, on the physics of the buttocks (giving rise to the proposed unit of measure of seat size: the Pinkwater), and giving practical advice as to the choice of automobiles. In the early 1990s Pinkwater voiced a series of humorous radio advertisements for the Ford Motor Company.

Following an appearance by Pinkwater on the Public Radio International program This American Life, his book The Devil in the Drain, ending up on banned book lists at numerous children's libraries.

Children's books

• The Artsy Smartsy Club
• Attila the Pun: A Magic Moscow Story
• Author's Day (1997)
• "Beautiful Yetta (2010)"
• Blue Moose (1975)
• Fat Camp Commandoes
• Fat Camp Commandoes Go West
• Fat Men from Space (1977)
• The Hoboken Chicken Emergency (recent editions ill. by Jill Pinkwater)
• The Last Guru
• Lizard Music (1976)
• Looking for Bobowicz: A Hoboken Chicken Story
• The Lunchroom of Doom
• The Magic Moscow
• The Magic Pretzel
• The Muffin Fiend
• The Neddiad (2007)
• The Yggyssey (2009); sequel to The Neddiad
• The Adventures of a Cat-Whiskered Girl (2010), sequel to The Yggyssey; also called The Vreemdelingenlied
• Slaves of Spiegel
• The Wuggie Norple Story (1980)
• The Magic Goose

Young adult/Teen novels

• Alan Mendelsohn, the Boy from Mars (1979)
• Borgel (1990)
• The Education of Robert Nifkin
• The Snarkout Boys books:
• The Snarkout Boys and the Avocado of Death
• The Snarkout Boys and the Baconburg Horror
• The Worms of Kukumlima
• Mystery Monster of Lake Ontario
• Young Adult Novel

Picture books

• Around Fred's Bed
• Bad Bears in the Big City : an Irving & Muktuk story
• The Big Orange Splot
• The Devil in the Drain
• Doodle Flute
• Ducks!
• Fat Elliot and the Gorilla (1974)
• Guys From Space
• The Irving and Muktuk Books
• Bad bears go visiting: an Irving & Muktuk story (2000)
• Irving and Muktuk: Two Bad Bears (2002)
• Bad bears in the big city: an Irving & Muktuk story (2005)
• Bad bears and a bunny: an Irving and Muktuk story (2006)
• Bad bear detectives: an Irving & Muktuk story (2007)
• The Larry Books
• Young Larry (1998)
• At the Hotel Larry (1998)
• Bongo Larry (1998)
• Ice Cream Larry (2000)
• Sleepover Larry (2000)
• Dancing Larry (2007)
• Pickle Creature
• Rainy Morning (ill. by Jill Pinkwater)
• Spaceburger: a Kevin Spoon and Mason Mintz Story
• Three Big Hogs
• Toothgnasher Superflash
• Wempires
• The Neddiad

Adult fiction

• The Afterlife Diet

Non-fiction

• Hoboken Fish and Chicago Whistle: a book of essays, combining essays from two previous books:
• Chicago Days, Hoboken Nights
• Fish Whistle
• Superpuppy: on raising a dog
• Uncle Boris in the Yukon and Other Shaggy Dog Stories