The Russian president referred to the Edinburgh-based author, who been criticised over her comments on gender identity, and talked about Russian authors being cancelled in the West.
Mr Putin said Ms Rowling had been cancelled "just because she didn’t satisfy the demands of gender rights".
He said: "They are now trying to cancel our country. I'm talking about the progressive discrimination of everything to do with Russia."
The Russian president went on to liken the situation to "cancel culture" Nazis trying to burn books in the 1930s.
JK Rowling trans row: Shutting down Harry Potter author is wrong way to win trans rights, says Wes Streeting
"We remember the footage when they were burning books," he said.
"It is impossible to imagine such a thing in our country and we are insured against this thanks to our culture. And it's inseparable for us from our motherland, from Russia, where there is no place for ethnic intolerance, where for centuries representatives from dozens of ethnic groups have been living together."
Ms Rowling responded by sharing an article about incarcerated Kremlin critic Alexei Navalny on Twitter. The author wrote: “Critiques of Western cancel culture are possibly not best made by those currently slaughtering civilians for the crime of resistance, or who jail and poison their critics.”
Ms Rowling also shared the hashtag #IStandWithUkraine.
In 2020, the Harry Potter author responded to an article headlined “Creating a more equal post-Covid-19 world for people who menstruate”, tweeting: “‘People who menstruate.’ I’m sure there used to be a word for those people. Someone help me out. Wumben? Wimpund? Woomud?”
She denies she is transphobic and has defended her comments by saying: “If sex isn’t real, there’s no same-sex attraction.” A message from the Editor:Thank you for reading this article. We're more reliant on your support than ever as the shift in consumer habits brought about by Coronavirus impacts our advertisers.If you haven't already, please consider supporting our trusted, fact-checked journalism by taking out a digital subscription.