Place2Be, which provides counselling and therapeutic services in primary and secondary schools, has merged with The Art Room, which for the time being will continue to operate from eight sites across Oxfordshire, London and Edinburgh.
The two charities said they intend to test out ways of integrating their services, and evaluate the impact to inform future developments.
Place2Be helps over 135,000 pupils and employs more than 1,000 volunteer counsellors. It also trains teachers in children's mental health issues.
The Art Room helps children with emotional and behavioural difficulties through art therapy. Many of the children who attend are disengaged from mainstream education, are disruptive, or need time away from a traditional classroom. It currently works with 530 children a week.
Catherine Roche, chief executive of Place2Be, said: "At a time when the profile of school-based mental health support has never been greater, we are pleased to be able to extend our offering for schools as part of a whole-school approach to mental health."
Lisa Harker, chief executive of The Art Room, added: "We are very excited by the potential for our two organisations to work effectively together, harnessing the strengths and potential of both organisations."