Atom Ant and Secret Squirrel aired independently of each other for the first part of the 1966–1967 season: Precious Pupp and The Hillbilly Bears aired as segments on The Atom Ant Show, while Squiddly Diddly and Winsome Witch aired as segments on The Secret Squirrel Show before recombining into the hour-long format in the winter. For the series' final NBC run under the Atom Ant/Secret Squirrel title, the show was one half-hour long.

The Hillbilly Bears cartoon segments were later repeated during the second season of The Banana Splits Adventure Hour (1969-1970), and all 52 Atom Ant and Secret Squirrel half-hours were syndicated as part of The Banana Splits And Friends Show, an umbrella title for a package combining episodes of several different Hanna-Barbera series (the other series included The Banana Splits Adventure Hour, The New Adventures of Huckleberry Finn, and The Adventures of Gulliver).