The details were revealed after a five-year-old Nottinghamshire boy recently returned to the classroom as a girl.
The Gender Identity Development Service (GIDS) said 969 under-18s have been referred in the UK in 2015-16, including nearly 200 aged 12 or under.
This compares to just 94 in 2009-2010.
*2015-16 figures, available for April-Dec only
The statistics also showed one three-year old and three four-year-olds were referred to GIDS since April last year.
In the Nottinghamshire case, letters were sent to classmates and parents at the start of the current term explaining the five-year-old's wishes to be treated as a girl.
Her family told the Nottingham Post the decision was not taken lightly and they had received support.
Nottinghamshire County Council admitted transgender issues were a new area for many schools but said it "supported head teachers on a range of equality issues".
Colin Pettigrew, the authority's director for children, families and cultural services, said: "Transgender is a characteristic protected by law and therefore head teachers across England continue to, and are required to, agree a clear plan to support the needs of transgender children and young people."
Updates on this story and more from Nottinghamshire
GIDS, based in north London, is the NHS's dedicated gender identity development service for children and takes referrals from GPs, paediatricians, mental health services and schools across the country.
Its director, Polly Carmichael, said in recent years more younger children were making gender transitions and there was no "right or wrong approach", with many families reporting their child was happier living in another gender.
However, she said research published in the Netherlands suggested that "for some young people who make an early social transition it may be difficult to de-transition if their gender identity develops in another direction".
In terms of the general increase in referrals, GIDS said there could be a number of reasons, but increased awareness and acceptance of gender issues - particularly via the media and social networks - was a likely factor.
Whatever age a child is referred, no physical changes can be made until the young person is in puberty, it said.
Bernard Reed from the Gender Identity Research and Education Society (GIRES)  - a charity which works to improve the lives of gender non-conforming people - said many young people still did not feel confident speaking about gender issues.
"There are several hundred cases each year and they are quite often referred for medical support" he said.
"But because society is often not supportive in such cases, usually these young people do not seek publicity".

Mr Yarrington, who served as governor from 1999 to 2005, had been on the run for almost five years.
The ex-governor is accused of taking millions of dollars in bribes from drug cartels in return for turning a blind eye to their smuggling activities.
A reward of 15m Mexican pesos ($800,000; £650,000) had been offered for information leading to his arrest.
Officials did not reveal how they located Mr Yarrington.
The attorney-general's office in Mexico said Mr Yarrington would be extradited to his homeland within days.
He is also wanted by the United States on charges of money laundering.
According to the US indictment, Mr Yarrington allegedly received large bribes from major drug traffickers operating in Tamaulipas, including the Gulf and the Zetas cartels.
In return, Mr Yarrington allegedly allowed the cartels "to operate their large-scale, multi-tonne enterprises freely, which included the smuggling of large quantities of drugs to the US for distribution".
Prosecutors say the bribes started when Mr Yarrington was running for governor and continued during his time in office, when he allegedly started investing the money in properties across the US border in Texas.
The indictment also accuses him of accepting cocaine in exchange for facilitating access to Mexican ports.
Before he went on the run, Mr Yarrington, who was a member of the governing PRI party before being expelled, said the charges against him were politically motivated.
He was not the only Mexican governor on the run.
Former Veracruz governor Javier Duarte, who is wanted on corruption charges, has been missing since October.
And in March, the ex-governor of Chihuahua, César Duarte, was declared a fugitive after he disappeared following allegations of corruption.
Both were expelled from the PRI party when the charges against them became known.
The number of children referred to the NHS with gender identity issues has increased significantly in recent years, according to figures obtained by the BBC.
[NEXT_CONCEPT]
Police in Italy have arrested the former governor of the Mexican state of Tamaulipas, Tomás Yarrington, 59.