James Van Der Beek provided voice work for a limited number of animated projects, with his most recognized role being in the English-language dub of a celebrated Japanese animated film. He voiced the protagonist Pazu in the 1998 Disney English-language dub of the Studio Ghibli film Castle in the Sky. In this science fiction adventure film, he stars opposite Anna Paquin, who voices the character Sheeta. His performance as the young orphan boy searching for the legendary floating city was noted for its effective conveyance of emotion and inflection, even as some critics observed that his vocal timbre sounded older than the character's intended age compared to the original Japanese performance.

Later in his career, Van Der Beek took on a regular voice role in children's animated television. From 2017 to 2021, he voiced the character Boris Hauntley in the Disney Junior series Vampirina. Boris is the father of the main character, Vee, and a member of a family of friendly vampires who move from Transylvania to Pennsylvania. This role placed him within the Disney animation landscape, marking a recurring collaboration with the studio across different decades. Aside from these two prominent credits, his involvement in anime or animated voice acting does not appear to include other major roles or recurring collaborations with specific directors or animation houses.