From 1 April 2004 the Chancellor of the Exchequer agreed to a return in grant aid of all VAT on eligible repairs and maintenance work carried out after 1 April 2004.
Application forms for grant assistance, together with detailed information about the scheme can be obtained from the Listed Places of Worship Scheme website.
For buildings other than listed places of worship (for example, church halls or unlisted churches) some building works can be zero-rated, providing the building works are eligible (for example, new build or installation of a disabled toilet) and the building is used for a “relevant charitable purpose”.
Your VAT-registered builder should give you an invoice showing where the exemption has occurred. They will need a certificate from you stating that you are a charity, and the building is used for charitable purposes.
The rules are complex and before issuing a certificate you should get copies of the relevant notices from HM Customs & Excise.