The "love message" was published online on Wednesday and has been signed by authors such as Jeanette Winterson and Malorie Blackman.
"We stand united with you, we hear you, we see you, we accept you, we love you", it says in the letter.
Transgender rights have been hotly debated in the UK recently and JK Rowling has played a prominent role.
Accused of transphobia
The author has been accused of being transphobic.
The storm of criticism picked up in June when she rallied that an article used the wording "people who menstruate" instead of "women".
Since then, Rowling has been subjected to hatred and even death threats, prompting 58 cultural figures - including author Ian McEwan and actor Frances Barber - to come out in her defense.