Pascha Thomas (pictured) says her daughter was sexually assaulted in the school bathroom by a student who was only able to be there because of a policy allowing gender fluid and transgender students to use whichever bathroom they chose

The Department of Education's Civil Rights division is investigating after a five-year-old girl was allegedly sexually assaulted by a boy in her class in November last year.

A complaint filed by the girl's mother alleges the child had gone to the bathroom, and the boy had been able to follow her because he identified as gender fluid and was, under school policy, allowed to be there.

The mother, Pascha Thomas, further alleges when she made a complaint to the school, she was told no action would be taken, and then child services was called on her.

When child services arrived at her door, a day after Christmas, Thomas says authorities told her the school had filed a report, but had named her as the responsible party.

'How do you, in your right mind, do something like that to a parent,' she said in a video filmed by conservative Christian group Alliance Defending Freedom [AFD].

'Their child has been sexually assaulted, then you turn around and paint them as the villain.'

Thomas joined forces with AFD before filing her complaint. The organization are well known for their stance against allowing transgender and gender fluid people to choose what bathroom or change room they use.

The five-year-old girl told her mother she was pushed against a wall and digitally penetrated through her pants, but Thomas says the school has taken no action

Her daughter, who told her mother she was pushed against a wall and digitally penetrated through her underwear by the other student, has not been named, and is referred to in legal documents as NT.

The complaint, filed by attorney Vernadette Broyles under Title IX law, alleges the district: 'created a hostile environment for girls by eliminating their expectation of privacy from the opposite sex (in the very facilities intended to protect privacy), and have exhibited deliberate indifference towards that hostile environment for girls'.

A school district spokeswoman appeared to dismiss Thomas' accusations and interpretation of the situation.

Speaking to Politico, she said the district was 'aware of the unfounded allegations', and 'we fully disagree with her characterization of the situation'.

'City Schools of Decatur is committed to supporting all students. We are aware of the unfounded allegations made by the Alliance Defending Freedom,' she said.

'We fully disagree with their characterization of the situation and are addressing it with the Office of Civil Rights. As this is a pending legal matter, we have no further comment at this time.'