Paint was thrown over the steps and front door of Our Lady's in Harryville on Saturday night. Police have said it is being treated as a hate crime.
The church has been the targets of vandals over many years. For a period in the 1990s, loyalists held weekly protests while Mass was being held.
Father Patrick Delargy said it was becoming a daily event for something to be thrown at the church.
"It's as much an irritation as much as anything else because it's one in a series of disturbances here round the church which have begun just before the twelfth of July.
"Almost every day there has been something thrown at the church or at the house.
"But this is the first time we've actually had anything straight on the church as far as the paint is concerned."
SDLP North Antrim MLA Declan O'Loan said: "Thankfully, it was not a serious incident but it was an unfortunate incident and one that is disappointing considering Ballymena has had a quiet summer when compared with other places."
Sinn Fein's Daithí McKay added: "Attacks on churches of all types are mindless and abhorrent and it is very sad that in this day and age Catholic churches in the Ballymena area are still being singled out as targets."
SIC: II