The presbytery was the middle layer of government in the Presbyterian Church, above session and below Synod. It comprised the ministers and ruling elders of the congregations affiliated to the presbytery. It dealt with matters that could not be settled at the level of session, either because there was a dispute of a nature that could not be resolved without recourse to a higher authority or because the issues related to more than one congregation. Presbytery meetings were held on a regular basis. Presbyteries were frequently reorganised. In addition, individual congregations could change presbytery if it meant that a dispute would be resolved.

The surviving minute book for the Presbytery of Strabane, covering the period 1717–40, reveals that the presbytery dealt with a variety of matters relating to the members of the congregations within its bounds. For instance, in December 1718 John Alison came before Strabane presbytery desiring a certificate testifying to his credentials as a good Presbyterian as he was preparing to emigrate. Presbytery decided not to issue him with one until just before he was ready to leave, and then only conditional on his continued good behaviour.

The Synod of Ulster was the highest authority in the Presbyterian Church in Ulster. It met once a year, usually in June, and was composed of representatives from every congregation in each of the presbyteries. The records of the Synod of Ulster meetings for the period 1690–1820 were published in three volumes by the Presbyterian Church in 1891 (available to read online at the Internet Archive). Much of the minutes deal with matters of a fairly routine nature. Occasionally, however, an item of real value will be recorded. From 1840, when the Synod of Ulster and the Secession Synod united, there are the printed minutes of the General Assembly, a set of which is in the library of the Presbyterian Historical Society.