£500-£10,000 grants will be offered to churches of any denomination to fix their buildings and keep them running.
The National Churches Trust will lead the 'Treasure Ireland' project, which will run over three years starting this summer.
The money can be used for repairs and maintenance to help keep churches in good condition and prevent expensive repairs.
Training and mentoring will also be offered to help people who look after places of worship.
This will include developing skills on writing funding bids, conducting maintenance and tourism to attract visitors.
The project aims to increase the number of people visiting churches in Northern Ireland for days out or as part of a holiday.
At least 100 churches will be added to the National Churches Trust's Explore Churches website which shows online users the architecture and history of Northern Ireland's religious heritage.
'Treasure Ireland' is funded jointly by the National Lottery Heritage Fund, the Pilgrim Trust, the Department of Communities and the National Churches Trust.
Michael Murray, deputy chief executive of the National Churches Trust said: "This project aims to change the dynamic of church heritage in Northern Ireland so that more churches and chapels can be kept in good condition and their architecture and history appreciated by more people."