The Crayon Shin-chan anime was originally conceived as a minor 'sacrificial' project meant to prop up another main show being pitched by ADK, and Shin'ei Doga's upper management reportedly told the staff to just 'make it last half a year'.

The production staff who created the Crayon Shin-chan anime originally worked on Fujiko F. Fujio anime like Esper Mami, Chimpui and 21 Emon; the show only came about after a scheduling conflict prevented another Fujiko anime from filling the new timeslot.

The very first episode aired with a low 4.0% rating, prompting producers to add the catchphrase 'Storm-calling' (Arashi wo Yobu) to the TV listings from the second episode onward just to make the show stand out in newspapers; ratings later skyrocketed to a record 28.2% in July 1993.

Because production was greenlit less than three months before the premiere, first director Mitsuru Hongo deliberately minimized the number of animation frames and used manga-like layouts to save time, even making things like the glass door plain blue instead of transparent.

Hongo abandoned the planned system of having a single chief animation director oversee the whole show just before the deadline, instead having one key animator handle an entire 7-minute segment as both key animator and animation director, a practice still used today, resulting in visibly different art styles between segments.

After 26 years, original Shin-chan voice actress Akiko Yajima stepped down at her own request in 2018; her successor Yumiko Kobayashi's performance was chosen partly because Kobayashi's voice acting in other anime like Duel Masters made her an easy fit for fans, resulting in surprisingly little backlash compared to typical voice-actor replacements in Japan.

After creator Yoshito Usui's sudden death in September 2009, the manga was left unfinished, but TV Asahi's president announced the anime would continue in the same manner as Sazae-san (an anime that keeps running after its creator's death); the first episode after his death began with a message of condolence.

Animation director Mamoru Oshii said that seeing the show for the first time made him think 'finally something as crude, violent, vulgar and dark as Bugs Bunny has appeared - something you're not supposed to show kids, exactly what I wanted to do,' and he reportedly volunteered several times to work as a guest staffer on the show but was turned down by the production team.

For the crossover episode with Shin Godzilla, the script originally had Godzilla emerge from the Arakawa River, but the location was changed to the Sumida River so that Godzilla, Tokyo Tower and Tokyo Skytree could all be shown in a single frame.

In South Korea, the manga was originally sold with an adults-only rating due to backlash from Confucian groups, and the anime dub heavily localizes the show by changing the setting to Seoul, making all characters Korean, and erasing or rewriting Japanese text into Hangul.