Due to the success of the animated series early on, many crew members went on to design and produce Superman: The Animated Series for the WB Network's children's block Kids' WB before making an additional 24 episodes of Batman: The Animated Series, better known as The New Batman Adventures, which aired alongside Superman: The Animated Series in 1997 following the end of Fox Kids' five year exclusive broadcast contract. The New Batman Adventures aired its final episode in 1999, but continued to air on the network into 2000.

In 1999, a new spin-off series, Batman Beyond, was released to further critical acclaim.[28] Then in 2001, the Justice League animated series was released, building on the success of both Batman: The Animated Series and Superman: The Animated Series and featured Batman as one of the founders of the League.

In addition, several of the animators from Japanese animation studio Sunrise worked on the series — their work on Batman: The Animated Series would become a great influence on one of their later series, Big O and the Cowboy Bebop episode "Pierrot le Fou".

Furthermore, the series had an immense impact on comics. Characters such as Renee Montoya and Harley Quinn were originally created for the animated series, but their popularity proved such that the characters were introduced into DC Comics (additionally, the character Harley Quinn appeared in the television series Birds of Prey and the newer animated series The Batman). The redesigned version of Clock King was later translated into the comics as well. While the character of Mr. Freeze was taken from the comics, his origin was redefined to make him a more tragic figure, and his popularity caused DC to bring the character back from the dead and then rescanned his origin to more closely match that of the series, as well as adding his wife into the comics. This same origin was used for the character in the live-action film Batman & Robin. Batman: The Animated Series was one of the first series to portray Bruce Wayne using a different voice while being Batman. It was also one of the first to suggest that Harvey Dent had a pre-existing dual personality before becoming Two-Face. This idea came from the show's producer, Alan Burnett.[29]

The dramatic writing and stylized art of Batman: The Animated Series sets it apart from traditional comic-book based cartoons. It can be considered the action-adventure equivalent of more mature cartoon shows like The Simpsons. For this reason the show's popularity (along with that of its various spin-offs) endures among older audiences and comic book fans.

The Lego minifigures of various Batman characters are more strongly based on the designs from Batman: The Animated Series than any other form of Batman media.[30] More precisely, the Joker, Two-Face, Poison Ivy, Mr. Freeze and Harley Quinn's minifigures seem to have identical costumes and faces to the characters from Batman: The Animated Series.

The dark atmosphere, mature themes, and even some of the voice cast from the series are heavily employed in the video game Batman: Arkham Asylum and its sequel, Batman: Arkham City.[31] Furthermore, the Animated Batman in this series will be an alternate skin for Batman in "Arkham City."