Dini wrote a number of episodes of the 1983–85 animated TV series, He-Man and the Masters of the Universe which years later became favorites amongst the show’s fans over the Internet, as well as contributing to interviews on the released box sets of the series, though Dini has made no secret of his distaste for Filmation and the He-Man concept. He wrote an episode for the Dungeons & Dragons cartoon in 1983; an episode of the Generation One Transformers cartoon series, “The Dweller in The Depths,” and an episode of the 1985 G.I. Joe cartoon called “Jungle Trap” and contributed to various episodes of the Star Wars: Ewoks animated series, several of which included rare appearances from the Empire. He also wrote the Jem episode “Music Is Magic” for the show’s second season.

During college, he began doing freelance animation scripts for Filmation, and a number of other studios. In 1984, he was hired to work for George Lucas on several of his animation projects. Dini later returned to the Star Wars universe in 2007 to script several episodes of Star Wars: The Clone Wars.

In 1989, Dini was hired at Warner Bros. Animation to work on Tiny Toon Adventures. Later, he moved onto Batman: The Animated Series, where he worked as a writer, producer and editor, later working on Batman Beyond. He continued working with WB animation, working on a number of internal projects, including Krypto the Superdog and Duck Dodgers, until 2004. In 1989 and 1990, he contributed scripts to the live-action television horror anthology series Monsters: “One Wolf’s Family” and “Talk Nice to Me”. Along with Bruce Timm he created the animated series Freakazoid!.

His graphic novel Dark Night: A True Batman Story, based on a mugging he experienced in 1993, was published in June 2016.

Dini and Bruce Timm introduced Harley Quinn in Batman: The Animated Series as her first appearance was the episode “Joker’s Favor” and in 1994, they adapted the character into comics in The Batman Adventures: Mad Love one-shot. Harley Quinn was integrated into the mainstream DC Comics continuity in the Batman: Harley Quinn one-shot published in 1999. Dini has written several comics stories for DC Comics, including an oversized graphic novel series illustrated by painter Alex Ross featuring Superman, Batman, Captain Marvel, Wonder Woman, and the Justice League. A hardcover collection of the Dini and Ross stories was published in 2005 under the title The World’s Greatest Super-Heroes.

Best known among Dini’s original creations is Jingle Belle, the rebellious teen-age daughter of Santa Claus. Dini created Sheriff Ida Red, the super-powered cowgirl star of a series of books set in Dini’s mythical town of Mutant, Texas. He collaborated with Kevin Smith on Clerks: The Animated Series. In 2001 Dini made a cameo appearance in Smith’s film Jay and Silent Bob Strike Back during the scene in which Jay and Silent Bob wear ridiculous looking costumes for a film being directed by Chris Rock, in which Dini says to them “you guys look pretty bad ass”.

He and Bruce Timm collaborated on the Harley and Ivy limited series for DC in 2004. Dini became the writer for DC Comics’ Detective Comics as of issue #821 (Sept. 2006) and created a new version of the Ventriloquist in #827 (March 2007). While Grant Morrison was starting a seven-year Batman story on the Batman title composed of long, interlinking arcs, Dini wrote a number of done-in-one stories over the following year as well as two crossovers with Morrison’s Batman, one focusing on the resurrection of Ra’s al Ghul and another on the return of Hush. After Morrison’s “Batman R.I.P.” storyline in 2009, creators were moved around titles and Dini started writing two new Batman titles Batman: Streets of Gotham and Gotham City Sirens. Streets of Gotham started and ended with story arcs about Hush while Gotham City Sirens focused on the women of Gotham; he wrote the bulk of both titles during their existence including the first and last issue of both.

In 2006 he announced that he was writing a hardcover graphic novel starring Zatanna and Black Canary. The following year he was the head writer of DC’s weekly series, Countdown. Dini co-wrote a draft script for the ill-fated Science Ninja Team Gatchaman movie, which never saw the light of day, resulting in him leaving the project. Dini wrote a series for Top Cow Productions, based in a character he created, Madame Mirage.

In July 2008, Dini started a partnership with GoAnimate to launch his Super Rica & Rashy series on the platform. Dini writes episodes released on the website on a regular basis. He lets anyone use his characters to create their own stories using the website’s online animation creation application.

On February 14, 2008 the first edition of Dini’s column, “200 Words with Paul Dini” was released on the iFanboy site.

He returned to write the animated version of Batman in Batman: The Brave and the Bold episode “Legends of the Dark Mite”. In the very same episode, he appeared in an animated form in comic book convention parody scene, where he was wearing Harley Quinn’s costume, along with Bruce Timm wearing Joker’s costume next to him. He would go on to write several additional episodes for the series, including “Chill of the Night!”, which contained a team-up between Batman and Zatanna, one of Dini’s favorite characters. Dini penned the storyline for the Rocksteady Studios video game Batman: Arkham Asylum, released on August 25, 2009. He wrote three episodes of Star Wars: The Clone Wars: “Cloak of Darkness,” “Holocron Heist,” and “Voyage of Temptation.”

Dini is the main creator of the Tower Prep series. On August 4, 2010, it was confirmed that Dini will be involved in Marvel Comics’ upcoming animated series Ultimate Spider-Man, which is set to air on Disney XD in 2012. He worked on Hulk and the Agents of S.M.A.S.H., an animated series centered around the Hulk and his supporting cast.

Dini and his wife Misty Lee appeared on Ken Reid’s TV Guidance Counselor podcast on April 6, 2016.

In September 2020, DC Comics announced that Dini would be among the creators of a revived Batman: Black and White anthology series to debut on December 8, 2020.