The Northern Synod consists of two presbyteries, the Pilgrim Presbytery of Northern Australia (PPNA) and the Northern Regional Council of Congress (NRCC).

The PPNA relates to the fifteen non-indigenous congregations across the synod. Three of these are congregation/patrols (Tennant Creek/Barkly, East Kimberly Ministry and Jabiru). Also, there are two patrols (West Kimberley and Centralian Patrol in the Centre) which do not have congregations.

The NRCC is a regional committee of the Uniting Aboriginal and Islander Christian Congress (UAICC) and a presbytery of the Northern Synod of the Uniting church in Australia. Representatives of more than 28 Aboriginal congregations make up the Council.