The children, two aged 11 and a ten-year-old, will appear in Belfast's Youth Court at the end of the month.
They were spoken to after the Church of the Holy Name at Station Road in Greenisland was badly damaged by a fire last Sunday evening.
The adjoining hall was destroyed and the roof of the church was also affected.
There was extensive smoke and water damage to the Church of Ireland building.
The congregation had held a service earlier in the day, celebrating 70 years in existence.
Police today confirmed that they were not treating the incident as a racially motivated incident.
The charges will be reviewed by the public prosecution service.
The children are due in court on Monday 30 September.