The minister of Greyfriars Kirk is a position within the Church of Scotland's Presbytery of Edinburgh and West Lothian. The most recent minister of Greyfriars Kirk was Richard Frazer, who was admitted in 2003 and retired in 2023. Interim Moderator for the vacant charge is Rev Dr Karen Campbell of Marchmont St Giles. Ministry is currently led by an Associate Minister. Under Presbytery plans, Greyfriars is due to unite with St Cuthbert's Parish Church in 2025.

Greyfriars originated in 1598, when Robert Rollock and Peter Hewat were appointed ministers of the South West Parish of Edinburgh, then meeting in the Upper Tolbooth portion of St Giles’. The charge of Greyfriars continued with two ministers until 1840, when St John's Church, Victoria Street, was erected and the last minister of the second charge, Thomas Guthrie became the first minister of the new church. New Greyfriars was erected in 1722 and occupied the western half of the kirk. It was a sole charge served by one minister. In 1929, the congregations of Old and New Greyfriars united under one minister. Both churches were burgh churches, meaning that the town council held the right to nominate the churches' ministers.

Since the establishment of the South-West Parish in 1598, 75 ministers have served the congregation: 40 in Old Greyfriars, 30 in New Greyfriars, and five in the united charge. Three ministers of Old Greyfriars were elected moderator of the General Assembly of the Church of Scotland during their incumbencies: George Kay in 1755, William Robertson in 1763, John Inglis in 1804. Two ministers of New Greyfriars were elected to this role during their incumbencies: Robert Henry in 1774 and James Nicoll Ogilvie in 1918. In 2003, Alison Elliot, an elder of Greyfriars, was elected to serve as moderator of the 2004 General Assembly. Elliot was the first woman moderator and the first lay person to hold the office since George Buchanan in 1567. Other notable ministers of Greyfriars include the Covenanters, Robert Douglas, Robert Traill, and Gilbert Rule; the statesman, William Carstares; the philanthropist, Thomas Guthrie; and the liturgical reformer, Robert Lee.

Old Greyfriars The first congregation of Greyfriars began as the South West Parish of Edinburgh, which met in the Upper Tolbooth portion of St Giles'. In 1620, the congregation moved to the newly-built Greyfriars Kirk. The designation Old Greyfriars was adopted after the erection of New Greyfriars in the western half of the Greyfriars building in 1722.

The congregation was served by two ministers until 1840, when St John's Church on Victoria Street was erected and the minister of the collegiate charge, Thomas Guthrie, became the first minister of the new church. Old Greyfriars was a burgh church of the city of Edinburgh, meaning that, until the abolition of patronage in the Church of Scotland in 1874, the town council held the right to nominate the churches' ministers.

Ministers of the first charge

15981599 Robert Rollock Previously a minister of Edinburgh; admitted, 18 April 1598; died in office, 8 January 1599.Scott 1915, p. 37.Dunlop 1988, p. 80. 15991610 Peter Hewat Translated from the second charge; appointed, 16 January 1599; removed to Little Kirk, 1610.16141641 Andrew Ramsay Admitted, 28 April 1614; translated to Old Kirk, 1640 or 1641.Scott 1915, p. 38. 1614 to 1620 was in St Giles, 1625 to 1641 was in Greyfriars16421647 George Gillespie Translated from Wemyss; admitted 23 September 1642; translated to the High Kirk, after September 1647.Dunlop 1988, p. 81. 16491662 Robert Traill Translated form Elie; admitted, 23 March 1649; imprisoned for ten months in Edinburgh Castle for engaging in a new Remonstrance, 23 August 1660; exiled by the Privy Council for high treason, 11 December 1662.1662 Robert Douglas Translated from the East Kirk and admitted, 2 June 1662; deprived for rejecting episcopacy, 1 October 1662.Scott 1915, pp. 38-39. 16621688Bryce 1912, p. 158. John Robertson Translated from Dysart; admitted, 6 November 1662; appointed almoner to Charles II, 24 March 1681; died, 11 January 1691.Scott 1915, p. 39.16891701 Gilbert Rule Called from a congregation in Dublin, 7 December 1688; admitted, 24 July 1689; appointed principal of the University of Edinburgh, 1690; died in office, 7 June 1701.Dunlop 1988, p. 82.17021729 James Hart Translated from Ratho; admitted, 20 September 1702; appointed almoner to George I, August 1726; died in office, 10 June 1729.Scott 1915, p. 40. 17301736 William Brown Translated from Lady Yester's and admitted, 23 July 1730; died in office, 23 March 1736. 17361745 William Robertson Translated from Lady Yester's and admitted, 10 October 1736; died in office, 16 November 1745.17471760 James Stevenson Translated from New Greyfriars and admitted, 24 December 1747; died in office, 17 July 1760.Scott 1915, p. 41. 17611793 William Robertson Translated and admitted from Lady Yester's, 26 November 1761; appointed principal of the University of Edinburgh, 1762; elected moderator of the General Assembly, 26 May 1763; appointed Historiographer Royal, 6 August 1764; died in office, 11 June 1793.Dunlop 1988, p. 83. 17941799 James Finlayson Translated from Lady Yester's; admitted, 9 January 1794; translated to the High Kirk, 14 March 1799.Scott 1915, p. 42.17991834 John Inglis Translated from Tibbermore and admitted, 17 October 1799; elected moderator of the General Assembly, 17 May 1804; appointed dean of the Chapel Royal, 23 February 1810; died in office, 2 January 1834.18341843 John Sym Translated from Sprouston and admitted, 24 September 1834; joined the Free Church, 1843.18431868 Robert Lee Translated from Campsie and admitted, 9 November 1843; dean of the Chapel Royal, 1846; died in office, 14 March 1868.Dunlop 1988, p. 84.Scott 1915, p. 43.18681876 Robert Wallace Translated from Trinity, Edinburgh, and admitted, 26 December 1868; demitted to become editor of the Scotsman, 1 August 1876.Scott 1915, pp. 43-44.18771909 John Glasse Ordained, 21 March 1877; resigned, 13 October 1909.Scott 1915, p. 44.19101916 Alexander Brown Grant Translated from Ecclesmachan and admitted, 10 May 1910; translated to Rosneath, 1916. 19171928 Samuel Dunlop Translated from Kilpatrick Irongray; admitted, 1917; died in office, 1928. In 1929, the charges of Old and New Greyfriars were united.

Ministers of the second charge

15981599 Peter Hewat Translated from Colinton; admitted as a minister of Edinburgh before 31 January 1597; readmitted, 18 April 1598; translated to the first charge, 1599. 16201622 Patrick Sands Principal of the University of Edinburgh; appointed, 1 December 1620; demitted, August 1622. 16221626 Robert Boyd Principal of the University of Edinburgh; elected, 18 October 1622; translated to Paisley, 1626.Scott 1915, p. 45. 1626 John Duncanson Appointed, 16 August 1626. 16301637 James Fairlie Professor of Divinity at the University of Edinburgh; admitted, 17 November 1630; elected to the Bishopric of Argyll and demitted, 28 July 1637. 16441660 Mungo Law Translated from the second charge of Dysart and admitted, 27 March 1644; taken prisoner by the English Army at Alyth, 28 August 1651; returned, January 1653; died in office, February 1660. 16641669 David Stirling Translated from Foulden; elected, 25 May 1664; demitted, 1669. 16691672 Alexander Ramsay Translated from Auchinleck; elected, 8 May 1669; translated to the High Kirk, 1672. 16721674 Alexander Irving Translated from West Kilbride and collated, 12 December 1672; demitted Whitsunday, 1674. 16741681 Alexander Ramsay Retranslated from the High Kirk; appointed, 14 June 1674; translated to the Old Kirk, 1681.Scott 1915, p. 46. 16811687 Alexander Malcolm Translated from Newbattle; instituted, 31 March 1681; translated to the Tron Kirk, 1687. 16871691 James Hutchison Translated from North Leith; elected, 11 August 1687; deposed "for contumacy", 1691. 16931702 John Hamilton Translated from Cramond and admitted, 1693; died in office, 17 October 1702. 17041707 William Carstares Principal of the University of Edinburgh; admitted, 8 November 1704; translated to the High Kirk, 28 December 1707. 17111715 Matthew Wood Translated from Leslie; admitted, 18 March 1711; translated to the Tron Kirk, 16 January 1715. 17211732 William Millar Translated from Lady Yester's; admitted, 22 January 1721; appointed dean of the Chapel Royal, 1727; died in office, 18 May 1732. 17321749 John Hepburn Translated from New Greyfriars and admitted, 14 December 1732; appointed almoner to George II, 13 February 1737; died in office, 29 April 1749. 17501754 Robert Hamilton Translated from Lady Yester's and admitted, 6 December 1750; appointed Professor of Divinity at the University of Edinburgh and demitted, 6 February 1754. 17541766 George Kay Translated from New Greyfriars and admitted, 11 October 1754; elected moderator of the General Assembly, 24 May 1755; died in office, 10 April 1766.Scott 1915, p. 47. 17671803 John Erskine Translated from New Greyfriars and admitted, 9 July 1767; died in office, 19 January 1803. 18041837 Robert Anderson Translated from Trinity College Kirk and admitted, 12 January 1804; died in office, 24 January 1837.Scott 1915, p. 48. 18371840 Thomas Guthrie Translated from Arbirlot; admitted, 21 September 1837; translated to St John's Church, 28 October 1840. On the erection of St John's Church, the charge of Old Greyfriars was uncollegiated.

New Greyfriars After an explosion destroyed part of Greyfriars in 1718, the town council decided to rebuild the church to accommodate two congregations. The western half of the church was occupied by New Greyfriars, which opened on 31 December 1722. In its earliest days, the congregation was also known as Wester Greyfriars.

Like Old Greyfriars, New Greyfriars was a burgh church and, prior to the abolition of patronage in the Church of Scotland in 1874, the town council held the right to nominated the minister.Dunlop 1988, pp. 24-27. Unlike Old Greyfriars, the congregation was a sole charge served by one minister. The town council often appointed promising ministers to the sole charge of New Greyfriars on the understanding that they would be promoted to one of the city's two-charge churches soon afterwards. For this reason, many ministers of New Greyfriars served relatively short incumbencies.Dunlop 1988, p. 85.