There are two types of charitable relief - mandatory and discretionary.
If the owner is a charitable institution and the development which would otherwise be chargeable to CIL is used wholly or mainly for charitable purposes by that owner (or by the owner together with other charitable institutions), the mandatory exemption at regulation 43 is engaged. There are three additional requirements, the development has to be occupied by or controlled by the charitable institution; the joint owner has to be a charitable institution; and the exemption must not amount to State aid under European law. If a charity is caught out by this final requirement, provided the charging authority has a discretionary charitable relief scheme and is satisfied that the State aid isn't aid that needs to be notified to and approved by the European Commission, exemption can be granted on a discretionary basis under regulation 45.
As far as discretionary relief is concerned, it is up to the charging authority whether to introduce a scheme (see the Trends and Themes article for more on this). If it does, there are still certain statutory requirements that must be met, including the requirement that trading activities from the development must be limited to the sale of goods donated to the charity where the profits are applied to their charitable purposes.
For more details, please get in touch and ask to see our CIL briefing "A Brief Guide to Charities".