She said five months of escalating bullying has had a "terrible effect" on her daughter.
The school said it took the attack "very seriously" and had expelled the pupil concerned and apologised to the girl's parents.
Greater Manchester Police confirmed it was investigating the shooting.
The woman told BBC Radio Manchester her daughter was shot by another pupil but was unhurt.
She said the girl had been physically attacked several times and was regularly abused and insulted.
"Our child came home to us in December and said she couldn't take any more and was going to throw herself off a bridge," said the mother.
"I had emailed the school about the escalation of the bullying and I don't think they dealt with it quickly enough - if they dealt with it sooner I don't think it would have escalated to this point."
A statement from the school confirmed a ball bearing pellet gun was fired at a pupil.
It added: "The matter has been treated very seriously and the pupil who fired the BB gun has been permanently excluded.
"We wish to send a message out to our community that this behaviour is completely unacceptable and will result in removal from our school.
"We have enlisted the support of a national organisation to help us further with our training of staff and pupils and support for our transgender pupils.
"We have met with the parents of the pupil to apologise and to see what we can do further as a school."
The mother of an 11-year-old transgender girl who was shot with a BB gun claims her school has not done enough to stop the bullying.