The character is being reimagined as a South Asian woman.
Kaling is both voicing the character and is an executive producer on the show, titled Velma.
"When it was announced that I was going to do the voice of Velma, people were very supportive and happy on Twitter," Kaling explained on Thursday's Late Night With Seth Meyers. "So I felt great because these are really intense fans -- cartoon, comic book fans."
In June, it was announced that the show was reimagining the character as South Asian.
"People were not happy," Kaling said of the update to the series. "There was a lot of, 'So, not Velma?' Those kind of tweets. 'Not the classic Velma that I'm always thinking about?'"
Kaling was surprised by the response to the animated mystery solver.
"First of all, I didn't know that she elicited such strong reactions in either direction," she said. "I just couldn't understand how people couldn't imagine a really smart, nerdy girl with terrible eyesight who loved to solve mysteries could not be Indian. There are Indian nerds. It shouldn't be a surprise to people, but people are like, 'No, no, no.'"
Kaling added that the backlash represented "a really small percentage of people," saying, "But it made me think, 'OK, we've got to be really careful with this character,' which we will be because we love her."
The Office alum is currently voicing the character of Val on the new Disney+ series, Monsters at Work, a spinoff of Monsters Inc. She shared her 3-year-old daughter, Katherine's, reaction to her mom's new animated role.
"She loves it," she said. "She's already, like, driven crazy with power. She's like, 'That's my mom!'"