St Peter's Church in Swepstone, Leicestershire, was targeted some time between Sunday evening and Monday morning.
Canon Vivien Elphick said everyone felt "gutted" as they had recently raised £25,000 for general repairs to the church.
A spokeswoman for Leicestershire Police said they were investigating.
The theft was discovered by builders who turned up to work on repairs to stonework at the church.
Canon Elphick said: "We just feel gutted in a sense.
"We have just spent £25,000 on the building and we now have to get a load more to pay for this.
"Fortunately we already had builders on site who have put sheeting over the roof otherwise rain would be going into the building right now."
A village church has had £50,000 worth of lead stripped from its roof by thieves.