| "Precedent Covenants" : Daniel Maclise's 'Marriage of Strongbow and Aoife' and the Writers of Irish history | McCafferty, John | Article in Book | University College Dublin Press | 2003 |
| "St Patrick for the Church of Ireland : James Ussher's discourse" | McCafferty, John | Monograph or Collective Volume | | 1997-1998 |
| 'Collegium S. Antonii Lovanii, quod Collegium est unicum remedium ad conservandam Provinciam' (Donnchadh Ó Maonaigh, 1617-18) | Mac Craith, Mícheál | Article in Book | Four Courts Press | 2009 |
| 'God bless your free Church of Ireland' : Wentworth, Laud, Bramhall and the Irish Convocation of 1634 | McCafferty, John | Article in Book | | 1996 |
| 'My experiences in the 1916 Rising' by Father Columbus Murphy, O,F,S,C, 29 July 1916 | Murphy, Columbus, O.F.S.C. | Article in Journal | | 2016 |
| A mundo valde alieni : Irish Franciscan responses to the dissolution of the monasteries, 1540–1640 | McCafferty, John | Article in Journal | | 2017 |
| Brigid of Kildare: Stabilizing a Female Saint for Early Modern Catholic Devotion | McCafferty, John | Article in Journal | | 2020 |
| Defamation and the church courts in early sixteenth-century Armagh | McCafferty, John | Article in Journal | | 1994 |
| Donatus Mooney's De Provincia Hiberniae (c. 1617) : Ireland, the Franciscan Island | McCafferty, John | Article in Book | | 2013 |
| Favourers, intercessors and patrons : why the Irish saints mattered so much to the Irish Franciscans | McCafferty, John | Article in Book | | 2015 |
| Franciscans and the Power of Fish in Seventeenth-Century
Ireland | McCafferty, John | Article in Book | Royal Irish Academy | 2024 |
| Impotence, violence, dowries and drinking: married couples in court in sixteenth-century Ireland | McCafferty, John | Article in Book | | 2019 |
| In the footsteps of long ago saints : Irish Capuchins in the Rhineland | McCafferty, John | Article in Book | | 2015 |
| Interview : Duffy of Dundalk | McCafferty, John | Article in Journal | | 2000 |
| Irish bishops, their biographers and the experience of revolution | McCafferty, John | Article in Book | | 2011 |
| John Bramhall and the Church of Ireland in the 1630s | McCafferty, John | Article in Book | | 1995 |
| John Bramhall and the reconstruction of the Church of Ireland, 1633-1641 | McCafferty, John | Thesis | | |
| John Bramhall's second Irish career 1660-3 | McCafferty, John | Article in Book | | 2009 |
| Luke Wadding : a life in and for books | McCafferty, John | Article in Book | NA | 2020 |
| Nicholas Archbold OFMCap : the small man with the big nose | McCafferty, John | Article in Book | | 2013 |
| People, politics and power : essays on Irish history 1660-1850 in honour of James I. McGuire | | Monograph or Collective Volume | University College Dublin | 2009 |
| Protestant prelates or godly pastors? the dilemma of the early Stuart episcopate | McCafferty, John | Article in Book | | 2005 |
| Recycling an island's past for a global Catholicism : Irish Franciscans in the seventeenth century | McCafferty, John | Article in Book | | 2022 |
| The act book of the Armagh diocese, 1518-22: a text and introduction | McCafferty, John | Thesis | | 1992 |
| The Act Book of the Diocese of Armagh, 1518-1522 : PRONI, MS DIO/4/2/11 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2020 |
| The Céli Dé - monastic reforms in 8th and 9th century Ireland | McCafferty, John | Article in Journal | | 1989 |
| The Churches and Peoples of the Three Kingdoms, 1603-1641 | McCafferty, John | Article in Book | | 2008 |
| The communion of saints and Catholic reformation in early seventeenth-century Ireland | McCafferty, John | Article in Book | | 2006 |
| The Irish Franciscans, 1534-1990 | | Monograph or Collective Volume | Four Courts | 2009 |
| The origins of sectarianism in early modern Ireland | | Monograph or Collective Volume | Cambridge University Press | 2005 |
| The Oxford History of British and Irish Catholicism, Volume I : Endings and New Beginnings, 1530-1640 | | Monograph or Collective Volume | Oxford University Press | 2023 |
| The reconstruction of the Church of Ireland : Bishop Bramhall and the Laudian reforms, 1633-1641 | McCafferty, John | Monograph or Collective Volume | Cambridge University Press | 2007 |
| The Wadding library of Saint Isidore's College, Rome, 1622-1700 | MacMahon, JosephMcCafferty, John | Article in Journal | | 2013 |
| To follow the late precedents of England : the Irish impeachment proceedings of 1641 | McCafferty, John | Article in Book | | 2001 |
| Venice in Cavan : the career of William Bedell, 1572-1642 | McCafferty, John | Article in Book | | 2009 |
| When reformations collide | McCafferty, John | Article in Book | | 2002 |