Scottish Health secretary Nicola Sturgeon unveiled the details of the NHS investment plan, which will help some of the country's most seriously ill youngsters.
The three-year National Delivery Plan for Children and Young People's Specialist Services, will look at ways to improve the care available for children with conditions such as cancer, cystic fibrosis and the gastric disorder Crohn`s disease.
Ms Sturgeon said the funding would "improve access to services and ensure they are provided as close to home as possible".
The plan highlights the Glasgow and Edinburgh children's cancer centres as immediate priorities. These, as well as the children's cancer centres in Aberdeen and Dundee, will receive money for more resources.
It is also hoped the investment will improve local cancer care at district general hospitals.
Other priorities of the plan include maintaining and developing the National Children's Bone Marrow Transplantation Service in Glasgow and expanding specialist adolescent services.
Under the plan health boards will be required to ensure that all staff, who routinely work with young people, have had appropriate training by 2013.