Speaking to The Telegraph, the Harry Potter star said he found the hatred directed at her “disturbing”.
“I can’t understand the vitriol directed at her,” Fiennes said.
“I can understand the heat of an argument, but I find this age of accusation and the need to condemn irrational.
“I find the level of hatred that people express about views that differ from theirs, and the violence of language towards others, disturbing.”
The actor’s comments come after the Harry Potter author came under fire last year for comments about trans people.
In June, Rowling tweeted about an article discussing “people who menstruate”.
The author commented: “I’m sure there used to be a word for those people. Someone help me out. Wumben? Wimpund? Woomud?”
The ensuing backlash and allegations of transphobia (which Rowling has denied) prompted the author to pen an essay defending her views on transgender issues.
“My life has been shaped by being female. I do not believe it’s hateful to say so,” she wrote.
“I know and love trans people, but erasing the concept of sex removes the ability of many to meaningfully discuss their lives.”
Fiennes’ comments defending Rowling differ from those from his Harry Potter castmates who have spoken out on the issue.
Stars Daniel Radcliffe, Emma Watson and Rupert Grint came out with statements of support for the trans community.
Radcliffe said: “Transgender women are women. Any statement to the contrary erases the identity and dignity of transgender people and goes against all advice given by professional health care associations who have far more expertise on this subject matter than either Jo or I.”