According to the NSPCC nearly 19,000 were taken to hospital because they had intentionally hurt themselves last year.
That's a 14% increase over the past three years, the charity said.
Injuries included cutting their bodies, overdosing on pills or burning themselves.
Rachel Welch is a Christian who works in mental health and told Premier the church had to be there to offer support.
She said: "This is about making sure that our youth workers are not only equipped but actually feel confident to deal with these issues.
"You don't have to be an expert in mental health to support young people. Just make space to listen to them and meet them where they are."
The NSPCC said its figures were "worrying" and were discovered through a Freedom of Information Request (FOI) to NHS Trusts and Health Boards.
Teenagers aged 13 to 17 are most likely to end up hospitalised for acts of self-harm, the statistics showed.
Childline was dealing with the equivalent of 50 phone calls a day from young people who were thinking about self harming, the charity warned.
Welch said that churches should "equip youth workers to spot the signs of "inner turmoil" like anxiety and depression "that might lead to an episode of self harm".
A Department of Health spokesman said: "We want children with mental health problems to get the help they need.
"That's why we are investing £1.4 billion to help every area in the country transform services for young people with all mental health conditions, including self-harm.
"We are also strengthening the links between schools and mental health services, and looking at how to improve services for self-harm in the reinvigorated suicide prevention strategy, to be published soon."
Listen to Premier's Antony Bushfield speaking to Rachel Welch: