Brendan Halligan was educated at St James's Christian Brothers School and Dublin Institute of Technology, in Dublin, and he graduated with a master's degree from University College Dublin in 1964. Following an early career as an economist, working with the Irish Sugar Company until 1967, he became involved in politics. In that year, he became General Secretary of the Labour Party.
He continued to serve as General Secretary of the party until 1980, and was appointed a Member of the European Parliament (MEP) from 1983 until 1984. During this period he was member of the Socialist Group, member of the Committee on Energy and Research, member of the Delegation for relations with the People's Republic of China.
In 1985, he was appointed as Chairman of the Irish Peat Development Authority, a position he held for ten years. Halligan served as Chair of the Sustainable Energy Authority of Ireland from 2007 until 2014. He is currently Chair of the Institute of International and European Affairs (IIEA), and he is also a Board Member of Mainstream Renewable Energy.