The girl, who has a mental age of seven, started at the school last September but in February her parents decided to pull her out after becoming dissatisfied with the support their child was getting and discovering she had spent a lesson alone in the toilet and no teachers had come to find her.
A spokesman for the school admitted this and apologised for the incident.
The girl has an Educational Healthcare Plan in place, which provides schools with additional funding to support a student’s needs.
Her father claims his daughter did not receive any support and wants to know where the money for his daughter has been spent.
Filey Ebor Academy says additional teaching assistant support was discussed in the autumn term but couldn’t be provided until January.
Gail Brown, chief executive of Ebor Academy Trust, said: “We take very seriously any allegations of procedures not being followed at our schools, especially with regard to our most vulnerable students.
“In this instance, as soon as these issues were raised, we immediately commissioned an independent, external assessor, with considerable experience of working with children with special educational needs and disabilities, to take forward the parents’ concerns as an impartial observer and understand if there are any lessons to be learned.
“This work has started. It is not something we are required to do, but I hope it helps underline the importance we place on always wanting to try harder for our children and their parents and carers.
“I am satisfied that Mr Cartmail and his team have done all they could for [this child], acknowledging at the same time that yes, of course, we can always do better.
“I sympathise with [her] parents who, quite rightly, want the best for their child and I apologise if they feel we have not delivered for them.”
Despite the offer of a place at Filey Ebor Academy still being available for his daughter, the girl’s dad said he and her mum weren’t comfortable with her returning there and would instead prefer her to go to a special school.
She has currently been out of education for three weeks and her parents have been relying on help from relatves to care for her during the day.
However, the family has recently been told by North Yorkshire County Council she has been allocated a place at a special school in the county from Easter onwards.
Jane le Sage, assistant director of inclusion at North Yorkshire County Council, said: “We are pleased to have achieved a resolution for the family.
"We try at all times to take account of the wishes of families and the needs of children in the provision of school places.”