The fund, launched in 2016, was created using £40m in funding from the Department for Digital, Culture, Media and Sport and The National Lottery Community Fund.
It aims to provide social action opportunities for 10- to 20-year-olds by distributing investment through working with other funders.
The new programme, which will be co-produced with young people, will provide funding to enable projects to specifically support children and young people facing multiple barriers and disadvantages.
- Interview: Simon Antrobus, Children in Need chief executive
- Funding: Children in Need main grants programme
The charities said young people will lead on the funding process and planning "ensuring their voices are heard and that the issues that matter most to them are addressed, while providing them with life-enhancing experience, new skills and confidence".
As part of the partnership, BBC Children in Need will also provide support for children and young people to embed social action into school life.
A new series of toolkits will be used in schools to inform pupils about social action and encouraging them to get involved in their communities.
The charity's chief executive, Simon Antrobus, said social action could transform the lives of children and young people, raising their confidence and self-esteem.
"As a charity we exist to support organisations in communities across the UK which empower children and extend their life choices, and this partnership with #iwill will go a long way in helping us making a lasting impact," he said.
James Harcourt, a director at the National Lottery Community Fund, said: "The partnership between the #iwill Fund and BBC Children in Need is a fantastic opportunity to put young people in the lead to tackle the issues that matter to them.
"Programmes that encourage social action are a great way to engage with young people, support them to build skills and overcome barriers," he said.
The #iwill Fund is part of the #iwill campaign launched in 2013 with cross-party and multi-sector support and co-ordinated by charity Step Up To Serve.
The initiative has attracted more than 900 partners from the public, voluntary, education and business sectors to support and deliver social action projects across the UK.