Two organisations are to spend £3.5m helping secondary and grammar schools in the Catholic and state sectors to share classes.
The International Fund for Ireland and Atlantic Philanthropies are making the investment after a successful trial.
For three years, 60 post-primary schools provided shared classes for Catholics and Protestants.
Afterwards, 74% of pupils said they enjoyed sharing classes with pupils of a different religion.
68% said they had made friends with children from the other community.
All the teachers surveyed said the scheme improved the quality of learning and range of subjects.
Another 58 schools will form partnerships to share education. Phase two of the scheme will include primary schools and special schools.
Earlier this month, the first minister Peter Robinson sparked a confrontation with the Catholic Church when he described the current education system in Northern Ireland as "a benign form of apartheid".
The head of the Catholic Principals' Association said Mr Robinson was guilty of "rabble rousing".