- Barnaby (1943)
- Barnaby and Mr. O'Malley (1944)
- Ruth Krauss, The Carrot Seed (1945), illus. by Johnson
- Harold and the Purple Crayon (1955)
- Is This You? (1955), co-written with Ruth Krauss
- Barkis: Some precise and some speculative interpretations of the meaning of a dog's bark at certain times and in certain (illustrated) circumstances (1956)
- Harold's Fairy Tale (1956)
- Harold's Trip to the Sky (1957)
- Terrible, Terrifying Toby (1957)
- Time for Spring (1957)
- Bernadine Cook, The Little Fish That Got Away (1957)
- Harold at the North Pole (1958)
- The Blue Ribbon Puppies (1958)
- Ellen's Lion: Twelve Stories (1959)
- The Frowning Prince (1959)
- Harold's Circus (1959)
- Will Spring Be Early? or Will Spring Be Late? (1959)
- A Picture for Harold's Room (1960)
- Harold's ABC (1963)
- The Lion's Own Story: Eight New Stories about Ellen's Lion (1963)
- We Wonder What Will Walter Be? When He Grows Up (1964)
- Castles in the Sand (1965), illus. by Betty Fraser
- The Emperor's Gifts (1965)
- Barnaby #1: Wanted, A Fairy Godfather (1985)
- Barnaby #2: Mr. O'Malley and the Haunted House (1985)
- Barnaby #3: Jackeen J. O'Malley for Congress (1986)
- Barnaby #4: Mr. O'Malley Goes for the Gold (1986)
- Barnaby #5: Mr. O'Malley, Wizard of Wall Street (1986)
- Barnaby #6: J.J. O'Malley Goes Hollywood (1986)
- Magic Beach (2005), with an appreciation by Maurice Sendak and an Afterword by Philip Nel
The Barnaby #1 to #6 books, published in paperback by Ballantine Books under the Del Rey imprint in 1985, were compilations of the first few years of the comic strip. Additional books were supposed to appear, but publication was suspended upon the death of Judy Lynn Del Rey.
A 1946 play, "Barnaby and Mr. O'Malley", was based on the comic strip. It played in several East Coast cities, attracting attention mainly for a scene in which O'Malley flew over the audience throwing out leaflets urging support for his Congressional race. Johnson said the child cast as Barnaby looked more like the cartoon Barnaby than any real child he ever expected to see,Producer...Barney Josephson;Script--Jerome Chodorov;O'Malley--J. M. Kerrigan;Barnaby--Thomas Wm. Hamilton;Jane...Iris Mann;McSnoyd--Royal Dano