The lead was taken from St Mary the Virgin church at Weston by Welland, about four miles north-east of Market Harborough.
The theft, which happened overnight on Sunday September 25 / Monday September 26, left large holes in the church roof, allowing water to pour through during the night.
Nicky Garratt, secretary to the Parochial Church Council (PCC), said: “One of the residents of the village, who is also a churchwarden, saw the gates to the churchyard were open on Monday morning.
“He went to investigate and discovered almost all of the lead from the flat roof on the north side of the church had gone.
“Underneath the lead, the church has a wooden slatted roof, so the rain just poured through.”
Nicky added that the church was surrounded by houses, and the busy B664, but no local residents had seen or heard anything.
She said the lead was worth thousands of pounds; perhaps up to £20,000.
The village has a population of under 150 people, so fundraising for the roof will be very difficult.
Church roofs are no longer fully insured, because of the frequency of lead thefts.
Insurers will typically pay the cost up to a set sum of perhaps £5,000, leaving the parish and the diocese to find the rest of the money.
Any passer-by who saw anything suspicious at the church should contact Northamptonshire Police.
That includes any sightings of a man seen inspecting the church on the morning of Friday, September 23.