Admissions of girls aged 10-14 have increased by almost 93% in the past 5 years from 3,090 in 2009/10 to 5,953 in 2013/14. In the same time there has been a rise in admissions of 45% in boys, from 454 to 659, according to the Health Behaviour in School-Aged Children report, which surveyed about 6,000 teenagers.
After the release of the findings, the government has said £30 million will be put into mental health care in accident and emergency units.
Lucie Russell from charity YoungMinds said: "These figures are sadly just the tip of the iceberg as many young people will be suffering in silence and not getting medical attention or support. For too long self-harm has been dismissed as something that is just an issue for teenage girls.
"We need to recognise that this is an issue for boys as well. Boys may often self-harm differently to girls, they may bang their heads or punch walls, and often this is seen as just aggressive behaviour rather than self-harm. Both boys and girls are under a lot of pressure and we need to make sure help and support is available for both them and their families as soon as they need it."
A World Health Organization (WHO) report due to be released in 2015 is expected to show the number of teenagers who have self-harmed has tripled over the past decade in England.
Of the 15-year-olds sampled, 22% said they had hurt themselves on purpose, while 43% said they self-harmed at least once a month.
Professor Keith Hawton, from the Centre for Suicide Research at Oxford University, wants schools to be bold by addressing the problem directly.
"We've got to think prevention here as well – what more can be done through schools to try and reduce the levels of self-harm through psychological wellbeing programmes," he said.
"These are being tested but I think this is really important. [It is] about prevention and not just treatment after the event."
As part of the Autumn Statement this month, the government announced it would invest more than £100 million in mental healthcare for young people over five years, with the intention of making it easier for them to get specialist help in their community.