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Presbyterian government of a church is typified by the rule of an assembly of presbyters, or elders. It was developed as a rejection of rule by hierarchies of single bishops (episcopalian church government). This theory of government is strongly associated with the Swiss and Scottish Protestant Reformation movements, with the Reformed churches, and more particularly with the Presbyterian church. John Calvin was influential in its formulation. Presbyterianism is constructed on specific assumptions about the form of the government intended by the New Testament: Thus, the governmental role of presbyters is limited to when seated together for decisions, and otherwise the office is for the service of the congregation, to pray for them and to encourage them in the faith. This theory allows flexibility in the practical outworking of government, which is opposed to the concentration of government in single bishops and concentration of the idea of the Church in hierarchical assemblies of bishops. Episcopacy and presbyterian forms are not compatible, mostly for historical reasons. Presbyterians sometimes admit that episcopacy was the form of government that developed very early in the church with practical causes, which for the practical reason of vulnerability to abuse ought to be reformed to conform more strictly to the biblical example. Some presbyterians are more adamant, that prelacy is in itself corrupt and rebellious against the word of God. Presbyterianism is distinguished from Congregationalism as well. The ordained ministry possesses responsibility for preaching and sacraments, government and practical care for the church, in a sense that the congregation does not have, although it is granted this responsibility for the sake of the local congregation.

In a Presbyterian church, elders make decisions for the local congregation, through a ruling body called the session (Latin sessio from sedere "to sit"). The members of the session are the minister (short for "minister of the Word and Sacrament", sometimes called a "teaching elder"), and the other elders (sometimes called "lay elders" or "ruling elders"). The elders are persons elected by the congregation and ordained for service by the minister and the laying on of hands by the elders currently serving. It is not uncommon for elders to be ordained for life, although this is not universally practiced.

Ministers are elders but have a distinct ordination, and a presiding role on the session. The relation between ministers and elders in terms of rank is very roughly comparable to the "bishop" and "priest" of Catholic tradition, however the other elders are rarely given a presiding role in preaching, baptism, or communion without special license from the "presbytery" (a regional assembly in which representatives of local sessions may vote). Also, the minister is not in any official sense the head of the session, and in fact, with only one vote, the minister is theoretically (although rarely in practice) governed by the session. The minister is a higher office, but not in a governmental sense; being regarded as "clergy", unlike the other elders (and the designation, "clergy", is not a politically correct term, among presbyterians sensitive to the historical meaning of that term). The English word, "priest" is derived by way of the Old English word prester from the Greek word, "presbyteros" (elder), from which the English language also has the word, "presbyter" . However, as with the words "bishop" and "clergy", the word "priest" is not normally used by Presbyterians to describe the office of any elder.

In presbyterianism there are sometimes further distinctions between the minister and the other elders. Some denominations of presbyterians consider the minister to be a member of the presbytery (in which case, it is called the "regional church"), rather than of the local congregation. Other presbyterian denominations enroll the ministers as members of their congregations.

The deacon is an office distinct from the elders. In the Presbyterian church, this service is distinct from rule in the church. The board of deacons is organized separately from the session, and is supervised and directed by the elders in doctrinal matters. Their role in all churches with presbyterian government is to carry out the ministry of mercy toward Christians within and outside the local congregation, and for others who are in need or distress, on behalf of the church. In other Reformed churches, the deacons may serve together with the elders in a ruling body called a "consistory".

Congregationalist churches are sometimes presbyterian also, with the difference that every local congregation is independent, and that aspect of the elder's office is emphasized in which he is regarded as a representative of the people in the affairs of the church. In full presbyterianism the congregations are united with one another by Presbytery, also called a Classis, and the Presbyteries and/or Classes are united in a General Assembly of all the churches. In contrast, congregationalists are therefore presbyterian only at the level of the congregations, which are united with one another by covenants of trust. Reformed Baptist churches are sometimes organized with presbyterian government, on the Congregationalist model.

Until the 20th century, only men had been eligible for the office of "teaching" elder (minister of the word and sacrament) or "ruling" elder, world-wide. This is widely not the case, any longer; although, it is usually considered a demarcation issue, distinguishing "liberal" from "conservative" churches with presbyterian government.

See also: Presbyterian church, Reformed churches, Congregationalist Church, Episcopalian government