The series was created to celebrate the 40th anniversary of Weekly Shōnen Jump and the 15th anniversary of V Jump, and was the third Yu-Gi-Oh! TV anime series following Duel Monsters and GX.

Original creator Kazuki Takahashi devised the setting, main characters, main monsters, and the design of the D-Wheels himself; he explained the D-Wheel concept was a natural choice since the story's scope expanded to a global scale requiring a means of transportation.

Takahashi created Riding Duels because he felt standard duels had been fully explored in the previous two series, so he wanted to introduce something new for a sequel.

Takahashi had intended to end the Yu-Gi-Oh! franchise with the previous series GX, but agreed to work on 5D's partly because the franchise had grown into a media mix beyond his sole control and because he was close with the anime staff.

The story concept originated from a one-shot manga Takahashi had drawn earlier, which already contained the core image of the Dark Signer arc: a giant enemy towering over a burning Nazca Lines geoglyph, confronted by five warriors fighting while riding motorcycles, with the idea that the five warriors would be reincarnated across generations.

Takahashi only provided story ideas up through the Dark Signer arc; the entire WRGP arc storyline was created solely by the anime staff, and Takahashi later praised the staff for the exciting buildup toward the finale.

5D's was the first Yu-Gi-Oh! anime series produced in high-definition, broadcast in a 16:9 digital HD format on digital terrestrial TV and in 16:9 letterbox format on analog terrestrial TV.

Starting from episode 15, the official Tele-Tokyo and Konami websites featured a segment called 'Duel One-Point Lesson' where the twins Leo and Luna comically explained duel rules, magic and trap effects using that week's broadcasted duel as an example.

The Synchro Monster mechanic introduced in the series proved highly popular in the real-world Official Card Game due to its powerful and versatile effects, and the 'BF (Blackwing)' and 'Infernity' theme decks used by characters became two of the dominant deck archetypes in both the video games and OCG world championships.

As in the previous series, viewer-submitted card designs were featured in the anime (used in episodes 74–78) and were later all turned into real Official Card Game cards.

The Black Rose Dragon card became notable as the only one of the six Signer Dragons ever placed on the OCG's limited card list (in September 2009), before being unlimited again a year later; Ancient Fairy Dragon later became the only Signer Dragon ever banned outright (January 2018), later returning as a limited card in 2023 after receiving an errata.

The Machine Emperors' Synchro-absorbing ability and the Iliaster three emperors' backstory tie into the anime's internal lore that a runaway Moment reactor, driven mad by human greed amplified through Synchro Summoning, led to humanity's destruction in a future timeline.

The American licensee 4Kids Entertainment heavily censored the series for The CW4Kids broadcast, removing depictions of discrimination against Satellite residents, torture scenes, and character deaths; episodes 36–41 focusing on the Arcadia Movement were restricted to online or adult-only broadcast slots, and the channel dropped the show entirely after episode 48 for a long hiatus before resuming it in 2010 as 'Yu-Gi-Oh! 5D's: Road to Destiny.'

The English dub skipped episodes 118 to 129 (the Team Taiyo/Team Ragnarok arc) and ended the series after episode 136 (the WRGP finals), rewriting the ending so that Z-one dies of despair after Aphoria's defeat, without resolving the Bruno/Antinomy or Sherry subplots; the Ark Cradle arc and final battle with Z-one were never dubbed or aired in English.

An early promotional anime short, 'Yu-Gi-Oh! 5D's: Evolving Duel! Stardust vs. Red Demons,' depicting the Yusei-vs-Jack duel, was screened at the 'Jump Super Anime Tour 2008' across 10 locations in Japan ahead of the TV series' broadcast, with a full DVD version bundled with a Konami card game product.