According to People, many social media users were outraged at her insensitivity.
"I hope @BetteMidler apologizes for her terrible transphobic comments and takes the time to educate herself on trans people's rights/dignity," one Twitter user wrote.
Another person tweeted, "@BetteMidler @IAmCait Just shows, you can be as gay-friendly all you want, but to some, transphobia comes so easy. How tired and pathetic."
Midler issued an apology that called it an "idle musing". She also tagged in the Human Rights Campaign which is a LGBTQ rights advocacy group.
Jenner sent her own tweet highlighting how grateful she was to E! and her friends for her time on the show.
People were still outraged in the Twittersphere though.
"Transphobia was never a 'temper of the times,' " one tweeter wrote. "It's always been wrong."
The Hocus Pocus star has certainly become witchier with age as it's not the first time she has had run-ins with the Kardashian-Jenner clan.
In March this year Midler criticised Kim Kardashian West about a provocative photoshoot.
"Kim Kardashian tweeted a nude selfie today. If Kim wants us to see a part of her we've never seen, she's gonna have to swallow the camera," she tweeted in reaction to Kardashian West's nude photo.
Haters gonna hate.
