| 1641 and the shaping of Cromwellian Ireland | Cunningham, John, 1984- | Article in Book | | 2012 |
| A Scramble for Ireland: Cromwell and the Land Settlement | Cunningham, John, 1984- | Article in Book | NA | 2021 |
| Anatomising Irish rebellion : the Cromwellian delinquency commissions, the books of discrimination and the 1641 depositions | Cunningham, John, 1984- | Article in Journal | | 2016 |
| Conquest and land in Ireland: the transplantation to Connacht, 1649-1680 | Cunningham, John, 1984- | Monograph or Collective Volume | Boydell and Brewer, for the Royal Historical Society | 2011 |
| Cromwellian County Mayo | Cunningham, John, 1984- | Article in Book | | 2014 |
| Divided conquerors : the Rump Parliament, Cromwell's army and Ireland | Cunningham, John, 1984- | Article in Journal | | 2014 |
| Early modern Ireland and the world of medicine: practitioners, collectors and contexts | | Monograph or Collective Volume | Manchester University Press | 2019 |
| Lay Catholicism and religious policy in Cromwellian Ireland | Cunningham, John, 1984- | Article in Journal | | 2013 |
| Oliver Cromwell and the 'Cromwellian' settlement of Ireland | Cunningham, John, 1984- | Article in Journal | | 2010 |
| Politics, 1641-1660 | Cunningham, John, 1984- | Article in Book | | 2018 |
| Sickness, disease and medical practitioners in 1640s Ireland | Cunningham, John, 1984- | Article in Book | NA | 2019 |
| The 1641 Rebellion in County Westmeath | Cunningham, John, 1984- | Article in Book | Geography Publications | 2022 |
| The Gookin-Lawrence pamphlet debate and transplantation in Cromwellian Ireland | Cunningham, John, 1984- | Article in Book | | 2011 |
| The history of medicine in early modern Ireland : some research problems and opportunities | Cunningham, John, 1984- | Article in Book | | 2019 |
| The transplanters' certificates and the historiography of Cromwellian Ireland | Cunningham, John, 1984- | Article in Journal | | 2011 |
| Transplantation to Connacht, 1641-1680 : theory and practice | Cunningham, John, 1984- | Thesis | | 2009 |
| Who framed Charles I? the forged commission for the Irish rebellion of 1641 revisited | Cunningham, John, 1984- | Article in Journal | | 2021 |