The Discovery Programme is governed by a Directorate (Board of Directors) and a Council, each of which is appointed for overlapping periods of 5 years. The membership of the Council is made up of the nominees of twelve bodies from across the island of Ireland which are involved in archaeological research. Each body is asked to nominate two persons – one female and one male – from which the Directorate makes the final selection, bearing in mind that not less than 5 members must be female and not less than 5 members must be male. The newly-appointed Council will serve until the end of 2013. The Council normally meets about 2 or 3 times a year, sometimes on its own but on occasions in joint session with the Directorate. The Directorate deals with the day-to-day business matters of the organisation while the Council is concerned more with reviewing the quality of its research and, at the appropriate time, appointing 5 members of the Directorate.

One other place is reserved for a National Museum of Ireland nominee and the chairman of the Council is ex officio the Chairman of the Discovery Programme, Dr Michael Ryan.