The charities said The Art Room, which runs art programmes to help children who have emotional and behavioural difficulties, had been transferred to Place2Be, which provides in-school support and training to improve the emotional wellbeing of pupils, families and school staff.
The two charities said that by working together they could extend and diversify the type of support they offered in schools.
The Art Room will retain its name and brand as part of the merger, at least in the short term, a spokeswoman for Place2Be said.
She said The Art Room raised the prospect of a merger because it wanted to increase its reach across the UK. Place2Be also wanted to extend and diversify the type of support it offered in schools, the spokeswoman said.
"The merger will provide a route to sharing The Art Room practice with many more schools in a sustainable way, ensuring that it can support more children," she said. "The Art Room will benefit from the greater capacity that Place2Be has in terms of business development, safeguarding, marketing, fundraising, communications and evaluation."
The Place2Be employs 454 people and had an income of £13.8m in the year to the end of March 2017. The Art Room has 33 employees and earned £970,205 in the year to 31 July 2016.
The spokeswoman said there would be no job losses as a result of the merger, which took place this month, and The Art Room would continue to run its services from eight sites in Oxfordshire, London and Edinburgh.
Lisa Harker, chief executive of The Art Room, will retain her role and join the Place2Be executive team. Catherine Roche will continue as chief executive of Place2Be.
Roche said: "There is an obvious and natural link between the work of our two organisations, and we are looking forward to exploring opportunities to integrate more closely in order to support more children and young people."
Harker said: "We are very excited by the potential for our two organisations to work effectively together, harnessing the strengths and potential of both organisations to support more children, schools and families in more effective ways."