The Chair of the Board of Trustees for Stepping Stone Projects is elected annually. Other members of the board are elected for a period of three years, after which they must be re-elected at the following annual general meeting.

The main board has two sub-committees, which deal with finance and personnel and policy development.

Day-to-day responsibility for the running of the charity is delegated to an Executive Management Team (EMT) consisting of the Chief Executive, a Director of Operations and a Head of Resources. The EMT is supported by a Senior Management Team consisting of four Operations Managers, an ICT Manager, a Management Accountant and a HR Manager.