More than 11,000 young people received counselling in 2017-18, the Welsh Government has said.
It comes as it also estimated three children in an average-sized classroom across the UK have a mental health problem.
Education Minister Kirsty Williams has announced a consultation aimed at tackling these issues.
Charity Barnardo's Cymru said the number of children it helped in the past year rose by 56%.
In 2018-19, it helped more than 1,000 children through schools-based counselling, therapy sessions and trauma recovery support - compared to 645 in 2017-18.
The charity also said 3,500 youngsters in Wales suffer from severe depression and 13% self harm, with at-risk groups including children in care, care leavers, young carers, minority groups and those who have suffered adverse childhood experiences.
Barnardo's wants more early intervention through government, councils and agencies working together.
"We see children and young people suffering from anxiety, depression, isolation and feelings of hopelessness," said director Sarah Crawley.
"Some are self-harming and others have suicidal thoughts.
"Young people's problems are made worse by the growing number of family breakdowns, the stresses brought about by poverty and the rise in social media which has led to online bullying and pressure to look or behave in a certain way."
Survey of 3,000 children, aged 11 to 19
44%didn’t find support at school helpful
56%wouldn’t feel confident approaching teachers or other staff
22%had accessed support for their mental health in school
48%wouldn’t know where to go to access support within school
Vale of Glamorgan Council commissions the charity to provide schools-based counselling to all six to 19-year-olds.
Two-thirds of the 500 asking for support posted a request in a special letterbox - with family issues the main concern, followed by anxiety and anger.
The council's prevention manager Mark Davies said: "There are many issues facing young people and we know their needs are greater now than they have ever been."
Barnardo's recently launched Golau on Anglesey, aimed at providing coping strategies and building resilience in 240 eight to 18-year-olds over the next three years.
There is also Beyond the Blue in Neath Port Talbot, giving help in schools and the community.
It comes as the National Assembly's Children and Young People Committee called for a "step change".
It wants more early interventions and ring-fenced funding for school-based support.
Betsan Roberts, 17, who is a member of the Welsh Youth Parliament described a "surge" in mental health problems in children as "quite alarming".
She said many schools took it upon themselves to address the problems, but more funding was needed.
Betsan, of Cardiff's Ysgol Gyfun Glantaf, said there could sometimes be a wait of up to six months see a specialist unless the matter was deemed urgent.
"But schools are taking it more seriously," she said.
"In my school, if you suffer from bad anxiety, you don't have to sit in the school hall for exams but teachers find a quieter room room for you."
Betsan described schools taking positive steps - such as a peer mentoring scheme at Glantaf - but more funding was needed to tackle issues.
The Welsh Government wants to "embed whole school approaches" and develop online help to complement face-to-face counselling.
As well as running a consultation until 18 December, £626,000 has been made available to councils to deal with waiting lists.
"Our national mission places wellbeing at the core of our new curriculum, supporting our children and young people to become healthy confident individuals, who are building their mental and emotional well-being by developing confidence, resilience and empathy," said Ms Williams.
An Estyn report from June suggested 33% of secondary and 66% of primary schools already adopt a whole-school approach to emotional wellbeing
They do this by offering classes and sessions to build resilience, promoting prevention and identifying signs early.
The Welsh NHS also provides support to schools through its specialist child and adolescent mental health services.
Cardiff University has set up a new research unit to look at why young people develop mental health problems.
Potential influences it will look at include whether parents and genetics play their part, as well as social media, wider lifestyle and environmental issues.
In the UK, one in eight young people experience anxiety or depression - a rise of 50% compared to 20 years ago - and the vast majority go unrecognised, according to the university's team.
Psychologist Fran Rice said the aim was to "develop new methods of ensuring there is adequate help and support early on".
This story has been inspired by questions from BBC Wales News readers about what is incorporated in the school curriculum to identify and tackle mental health, anxiety, stress and self esteem?
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