Guernsey Police said an unidentified male broke into the St Peter Port premises, causing damage and stealing items, between 23:00 GMT on Friday and 00:30 the next day.
Money from charitable donations was among the items taken.
The Reverend Penny Graysmith said the man had caused "disrespect to the building and the people who care for it".
'Deeply sad'
She described how she arrived at the church on Saturday morning to find "thousands of pounds of damage".
Ms Graysmith said: "The donations tube had been dragged right across the building, scratching our glorious 200-year-old floor, and taken to the far side of the building where it had been smashed and money had been taken."
She said it was difficult to tell how much money had been stolen but a donation box for the GSPCA was also taken.
She said: "The church showcased almost 40 charities, so the generosity and the kindness of the people of the bailiwick was there for all to see and enjoy.
"It's such a stark difference when one selfish individual breaks in, causes huge damage and disrespect to the building and the people who care for it, it's deeply sad."
Guernsey Police has begun an investigation.