Presbyterian polity is the defining structural characteristic of this tradition. Governance is by presbyters (elders), organized in four courts: the session (governing the local congregation), the presbytery (governing a regional grouping of congregations), the synod (an optional intermediate court in some bodies), and the general assembly (the highest court, composed of commissioners from presbyteries). This collegial, representative structure is understood as reflecting the New Testament pattern of churches governed by a plurality of elders, without bishops having personal jurisdictional authority over multiple congregations.

The Westminster Confession (Chapter XXV–XXXII) and Form of Government specify this polity in detail. Christ is the sole head of the church; the church governs itself under his authority through the appointed courts. Presbyterianism rejects both Congregational polity (where each local church is autonomous) and Episcopal polity (where bishops have hierarchical authority). The marks of the true church in the Westminster tradition are the preaching of the Word, right administration of the sacraments, and exercise of church discipline. The general assembly has legislative authority binding on member churches, exercised by elected commissioners rather than ex officio leaders.