The Church of Scotland has a Presbyterian structure, which means it is organised under a hierarchy of courts. Traditionally there were four levels of courts: the Kirk Session (at congregational level), the Presbytery (at local area level), the Synod (at a regional level) and the General Assembly (the Church's highest court). However, the synods were abolished in the early 1990s.

Scottish local government was reorganised in 1975, creating a new system of regions and districts to replace the long-standing counties and burghs. The General Assembly of the Church of Scotland also ordered a major reorganisation of presbyteries in the mid-1970s, redrawing presbytery boundaries to make them broadly contiguous with the then-new local government boundaries. An example was the union of the former Presbyteries of Cupar and St Andrews, creating a new Presbytery of St Andrews (which also included the Parishes of Newport-on-Tay, Wormit and Tayport, previously in the Presbytery of Dundee). This new Presbytery's boundaries mirrored the North East Fife District Council.

Following further local government reorganisation in the 1990s (replacing regions and districts with a single-tier system of councils), it was proposed to further considerably reduce the number of Presbyteries (possibly to as few as seven). This proposal was rejected by the General Assembly. Since 2003 several presbyteries have voluntarily sought permission to merge, as described below. Despite these mergers the existing Presbytery numbering system is being retained, albeit now with some gaps.

It is the presbyteries which have oversight of parishes and pastoral responsibility for parish ministers, and the Kirk Sessions of the individual parishes are subordinated to them. A parish minister is answerable to the Presbytery, not to the Kirk Session. The following is a list of presbyteries, arranged according to historical synod, and with the presbytery code number from the Church of Scotland Yearbook.

The Church of Scotland is currently in a process of consultations with the aim of reducing the number of presbyteries to around 12. The current completed mergers, as at February 2021, are as follows:

On 1 June 2020 the presbyteries of Aberdeen and Shetland merged to form the Presbytery of Aberdeen and Shetland ( with Shetland reducing its parishes to one ) On 1 September 2020 the presbyteries of Dumbarton and Greenock and Paisley merged becoming the Presbytery of The Clyde. On 1 January 2021 the presbyteries of St Andrews, Kirkcaldy and Dunfermline merged becoming the Presbytery of Fife. On 1 January 2023 the newly formed Presbytery of Perth unites the former presbyteries of Angus, Dundee, Dunkeld and Meigle, Perth and Stirling.