Secret Squirrel is a parody of the spy genre, with most shorts spoofing elements of the James Bond films; his designation 'Agent 000' is itself a play on Bond's 007.

The character's archenemy Yellow Pinkie is a parody combining Auric Goldfinger from Goldfinger and Sydney Greenstreet's Kasper Gutman character from The Maltese Falcon.

Secret Squirrel debuted in a prime-time animated special called The World of Secret Squirrel and Atom Ant, which aired on NBC on September 12, 1965, before getting his own show in 1966.

In the original series, Morocco Mole's voice by Paul Frees was an impersonation of actor Peter Lorre.

For the 1993 reboot Super Secret Secret Squirrel, original voice actors Mel Blanc and Paul Frees could not return since both had died, so Jess Harnell and Jim Cummings were cast as Secret Squirrel and Morocco Mole respectively.

The 1993 revival swapped the characters' original personalities: Secret Squirrel, once a bumbling agent, became competent and effective, while Morocco Mole, once more intelligent and a chauffeur-type figure, became the clumsy, childlike sidekick.

2 Stupid Dogs creator Donovan Cook was asked by new Hanna-Barbera president Fred Seibert to revive a classic studio cartoon within his new show, and chose Secret Squirrel because it was one of his personal favorites, resulting in the Super Secret Secret Squirrel segments.

In 1966, Hanna-Barbera Records released an LP titled 'Secret Squirrel and Morocco Mole in Super Spy,' on which Mel Blanc reprised his role as Secret Squirrel but Daws Butler voiced Morocco Mole instead of Paul Frees.

The phrase 'Secret Squirrel stuff' is used within U.S. intelligence circles to lightheartedly refer to highly classified material, a slang usage inspired by the cartoon character's name.