Director Kenji Kamiyama, a former student of Mamoru Oshii's studio, conceived the series as a parallel world premise: what if Motoko Kusanagi had never met the Puppet Master and had remained in Section 9. This makes it a distinct 'third' version of Ghost in the Shell alongside the original manga and Oshii's film.

The series was produced with an 800 million yen investment, and original manga author Masamune Shirow contributed plots for several episodes, character and mechanical sketches (including designs for the Tachikoma), and approved the scripts before production.

For the second season, 2nd Gig, Mamoru Oshii contributed ideas to the overall concept and initial planning, supervising the series and writing plots for each episode.

Writer Dai Sato explained that the 'Individual Eleven' storyline was originally meant to explore how Japan might participate in war after 9/11, but by production time the Iraq War had started and Japan's Self-Defense Force had been deployed, leading him to use the episodes to comment on the irresponsibility of Japanese voters who elected politicians sending troops abroad.

The opening theme 'Inner Universe', composed by Yoko Kanno and performed by Origa, features lyrics in Russian, English, and Latin.

When Stand Alone Complex was rebroadcast on Japanese terrestrial television, the original opening and ending themes were swapped for alternate versions, replacing 'Inner Universe' with 'GET9' and 'Lithium Flower' with 'I Do', the latter having originally been an insert song from 2nd Gig.

On 6 November 2004, long before the global anime boom, the series topped every demographic ranking (male viewers aged 12-17, 12-24, 12-34, and 18-24) among all US commercial cable television, making it an early spearhead for Japanese anime's overseas popularity.

Following the death of opening theme singer Origa in early 2015, some 2015 reruns of the series on TV Saitama overlaid a memorial message honoring her during the opening or the start of the episode.

The 'Laughing Man' storyline draws heavily on quotes from J.D. Salinger's novel 'The Catcher in the Rye', which Togusa discovers referenced during his undercover investigation.

Three episodes (10, 11, and 19) were deemed unsuitable for broadcast standards and were skipped when the series aired on terrestrial Nippon TV in 2004, despite airing uncut on the pay-per-view Perfect Choice service in 2002.