Tara Hudson, 26, from Bath, was sentenced to 12 weeks in jail after admitting assault.
She has had reconstructive surgery and lived as a woman all her adult life but, because she is legally a man, was sent to the all male HMP Bristol.
Her supporters claim it has placed her in danger of abuse and sexual violence.
Hudson was sent to prison on Friday after pleading guilty, at Bath Magistrates' Court, to an assault by beating on 26 December last year.
Her mother, Jackie Brooklyn, said the prison sentence came as a "shock".
"When they said they were taking her to [HMP Bristol at] Horfield I was horrified.
"I don't think she'll cope with it very well. She's lived as a woman for so long. She is a woman.
"To be put into an all male prison, it's like me being put into a male prison."
The online petition, calling for Hudson to be transferred to a female jail, claims she "is in extreme danger of abuse, sexual violence, and even death".
A report published earlier this year found levels of violence at HMP Bristol had "risen sharply" and not enough was being done "to protect some vulnerable prisoners".
A second petition in support of Hudson has received more than 3,000 signatures.
A Prison Service spokesperson said: "It is longstanding policy to place offenders according to their legally recognised gender.
"There are strict rules in place to ensure transsexual prisoners are managed safely and in accordance with the law."
A petition calling for a transgender woman to serve a prison sentence in a female prison has attracted more than 10,000 signatures in under 24 hours.