The boy was denied proper education for two years following a string of failings by Dorset County Council, which put him "at risk of harm due to a lack of proper procedures in place", the Local Government and Social Care Ombudsman found.
The ombudsman's report details how the boy is on the autistic spectrum and has attention deficit hyperactivity disorder, and after he struggled with mainstream education, the council attempted to offer him alternative education provision in 2015.
During this time he attended a community farm but nine months later it was discovered that it was not registered with the education regulator.
Two months after being removed from the farm, he was then sent to a private setting specialising in supporting children with autism and special needs.
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However, the boy's parents were forced to remove him over concerns that it did not offer full-time schooling, and over the quality of education and behaviour of other pupils.
A further attempt was made by the council to educate the boy with four hours' tuition a week, but this only lasted a month.
In addition, throughout the boy's ordeal his special educational needs and disability (SEND) education, health and care (EHC) plan was not updated.
Eventually, in April of this year, the community farm he had attended received its registration and the boy returned there part time, with additional home tuition offered.
Ombudsman Michael King's report is critical of the council's handling of the boy's case, in particular failures around assessing his needs through his EHC plan.
The council did not follow the annual review process correctly, failed to arrange suitable alternative education and was poor in its handling of a complaint made by the boy's father, states King, adding: "From the start of secondary education in September 2015, the council should have kept the boy's EHC plan under review.
"But despite multiple triggers, it did not even consider conducting a reassessment - leaving him with the same EHC plan since primary school.
"Consequently, the boy has been out of full-time education for two years, affecting his ability to take his GCSE exams and his future prospects.
"His father has told us his son has spent a considerable time isolated at home, setting back his education, increasing his anxiety and adversely affecting his confidence and independence.
The ombudsman is also concerned about the council's wider support for children with special educational needs, noting eight further failures since March 2018.
"Unfortunately, this is not the first complaint we have upheld about the council's provision for children with special educational needs: we have found fault on eight separate occasions since March 2018.
"I am concerned the council is not learning from these cases, and it suggests there are wider systemic issues that need to be addressed."
The county council was abolished on 31 March 2019 as part of structural changes to local government in Dorset, and Dorset Council is now responsible for the redress.
The ombudsman has ordered the council to apologise to the boy and his family as well as allocate £4,000 specifically for his day-to-day education and consult with his parents on how the money is to be spent.
The council has also been ordered to pay the boy £1,000 for the distress its failures have caused him. His parents have been awarded £300 each.
However, King does note that the council is taking steps to "address the problems I have found in this and earlier cases".
This includes ensuring the council develops and issues staff with guidance around EHC needs and assessment and help for staff in finding secure alternative education provision.
"We fully accept the ombudsman's findings and apologise to the family for the stress and disruption caused, particularly to the young person involved," said Andrew Parry, Dorset's portfolio holder for children, education and early help.
He added: "We have a new director and new head of education & learning and are working with schools to provide more alternative education for children with additional needs in Dorset.
"We're also reviewing our internal processes to improve the way we support families. We have a lot of work to do but we're determined to make things better for children and families."