Befriend a Child is set to go into secondary schools and help mentor pupils.
The charity is working in partnership with MCR Pathways in Glasgow to launch the project in the city.
The scheme is designed for children in S3 and S4, with the aim of reducing exclusion, increasing attendance and improving achievement towards a positive destination.
Selected volunteers are to be trained and then will be able to help children who are at risk.
Secondary schools including St Machar, Torry and Kincorth will benefit from the plans.
The windfall of £50,000 came from Bill and Lorraine Budge, of Aberdeen, from their Budge Foundation and will be delivered over five years.
The foundation supports organisations whose focus relates to the wellbeing and education of children worldwide.
Jackie Hothersall, CEO of Befriend a Child, said the money will help the organisation make a positive impact in children’s lives.
She said: “The support will enable us to both deliver and develop the service with the confidence that funding is in place.
“We are grateful that the Budges recognise the acute funding challenge we, like other charities, face and we can’t thank them enough for showing faith in our mentoring service.
“Building on the fantastic results MRC Pathways has already delivered in Glasgow schools, and on our own success in Aberdeenshire schools, we are excited about bringing this service to Aberdeen city.
“With the benefit of the Budges’ long-term support we plan to make it a success here too.”
The charity is currently on the lookout for volunteers who would like to be involved with the MCR Pathways mentoring and has asked anyone who is interested to get in touch.
Lorraine said: “I was first made aware of Befriend a Child through working on the Children’s Panel.
“I saw first-hand what a befriender could do for a child and giving this money means that we can look to engage older children into their education.
“The project will hopefully provide a spark for them and allow them to attend school more and stay on the right path.”