O'Malley was born in Dublin. His website states, "He was educated at University College, Dublin, and at Yale, Tufts and Harvard universities in the United States.
At the University of Massachusetts Boston, he is the John Joseph Moakley Professor of International Peace and Reconciliation at the John W. McCormack Graduate School of Policy Studies; a Senior Fellow in the Center for Development and Democracy; and the founder and editor of the New England Journal of Public Policy, a semiannual publication of the McCormack Graduate School. He is also a Visiting Professor of Political Studies at the University of the Western Cape in South Africa.
O'Malley spent time in Northern Ireland in the 1970s and 1980s, during "The Troubles", a period of sectarian strife and violence. He became interested in the way that South Africa, also facing internal division, had gone from apartheid to a racially integrated democracy without a civil war. In 1992, he participated in bringing some of the South African figures in that transition to Boston, Massachusetts for a meeting with representatives of the factions in Northern Ireland. In 1996, he helped arrange a second such meeting, in Belfast, attended by South Africans Cyril Ramaphosa of the African National Congress and Roelf Meyer of the white National Party.
In 2007, based on these experiences, O'Malley became involved in working toward reconciliation within Iraq. He helped arrange a conference at a resort in Finland, where 16 Iraqis met with experienced negotiators from South Africa and Ireland who described the processes toward peace in their countries. O'Malley's role included recruiting the Iraqi participants, then roaming around Baghdad with $40,000 in cash and covertly procuring their airline tickets. The Iraqis concluded the meeting by agreeing among themselves on a statement based partly on the Mitchell Principles developed during the Northern Ireland peace process. The Boston Globe reported:
As news of the Finland conference spread, skeptics were quick to point out that few of those in attendance had real power in Iraq, either in mainstream politics or in the various armed groups. O'Malley responds that this approach to conflict resolution is a progression, that there is an initial feeling-out process, and that follow-up sessions begin to draw a broader, more influential cast of characters.
O'Malley has monitored elections in South Africa, Mozambique, and the Philippines on behalf of the National Democratic Institute for International Affairs. He is also a frequent contributor to The Boston Globe.