They were chosen from 16 applications and it is expected that 10 campuses will be created over the next five years.
The three projects are Moy Primary School and St John's Catholic Primary in Moy; St Mary's High, Limavday, and Limavady High School and Ballycastle High and Cross and Passion college.
In January 2014,  Education Minister John O'Dowd  launched the Shared Education Campuses Programme, with a deadline of 31 March for a receipt for expressions of interest.
On Tuesday, the minister said:  "I believe shared education has the potential to deliver real educational benefits, to ensure best use of resources and to further community cohesion.
"The Shared Education Campuses Programme provides schools with the opportunity to build on existing sharing arrangements and access funding to help improve or provide shared facilities.
"We received a significant level of interest in this programme with 16 applications. I am pleased to be in a position to announce the first three projects to be supported."
Mr O'Dowd said: "The three projects selected will build on well established sharing arrangements between the schools involved and will help embed and enhance those sharing arrangements.
"This was the first call for projects and I am conscious that the limited time meant not everyone was able to have proposals worked up in time for the deadline.
"Therefore, as well as approving the three projects to be advanced through to a detailed business case, I am announcing that a second call for projects will open in September this year.
"Those that were unsuccessful in this announcement will receive feedback on their proposal and can resubmit it, if appropriate, to this second call."
The successful projects will now  proceed to the planning stage.
Three sets of schools have been selected by the Department of Education in Northern Ireland for new shared campuses.