For most people the problem will resolve before adulthood but for 10% it will continue into their adult lives.
Teenage girls are more likely to self-harm than boys and are at greater risk of continuing as young adults.
The Lancet study findings have important implications for the treatment of mental health issues and prevention of suicide in young adults.
The study looked at almost 2,000 adolescents in Australia, repeatedly surveying them over a period of 15 years.
Researchers found that anxiety, depression, heavy alcohol use, cigarette smoking and cannabis use were all associated with self-harm.
The study suggests that self-cutting and burning were the commonest forms of self-harm during adolescence.
As 90% of teenagers who self-harmed stopped before they reached adulthood, the research should offer some reassurance to families, schools and clinicians, the authors of the study say.
But, Marjorie Wallace, chief executive of the mental health charity SANE, said:
"The figures showing that 90% have stopped by the time they reach their twenties should not seduce us into thinking that self harm is just a phase that young people will grow out of".Suicide risk?
"Our research shows that counter to common perception, people self-harm and continue to self-harm at times throughout their lives to protect themselves from attempting suicide and their families and friends from experiencing their mental pain."
Because of the association between self-harm and suicide, the researchers suggest treating common teenage mental health problems could be part of an "important and hitherto unrecognised component" of preventing suicide in adults.
"Self-harm is one of the most significant predictors of completed suicide, " a lead author, Dr Paul Moran, of King's College London, said.Continue reading the main story
In cases of self-harm it is vital to discover what is driving the child to take such drastic action ”End Quote Sue Minto Head of ChildLine Of the people who have died by suicide, around 50-60% have a known history of self-harm, according to Professor Keith Hawton, Director of the Centre for Suicide Research, University of Oxford.
How many people who have self-harmed die due to suicide, is less clear.'Hidden population'
But Professor Keith Hawton, who was not involved in the study, said the findings could broaden the focus of the Suicide Prevention Strategy for England, which he is working on.
"We now know from studies like this one..... that there is a very large population of youngsters who are self-harming in the community. And we estimate about one in eight of them go to hospital. So this is the hidden population," he said.
"Though a focus on hospital management is crucial, what we should perhaps be thinking more of is the management of self-harm at a community level, particularly how schools respond and how families can be helped to respond," he said.
The authors say it is important that people living or working with young people are able to spot signs of distress and find the help they deserve.
"Otherwise there may be persistent ramifications in later life," Dr Paul Moran said.
Sue Minto, Head of ChildLine, which last year dealt with 30,000 contacts from children about self-harm, suicide and depression, said:
"In cases of self-harm it is vital to discover what is driving the child to take such drastic action. Something is obviously making them extremely unhappy or frightened and until this is resolved it is likely they will continue to injure themselves or, in extreme cases, be driven to suicide".