Born in Ireland on 1 April 1828 to Patrick Flanagan (hatter and woolsorter) and Martha Dufficy (daughter of Henry Dufficy - farmer), he and his family emigrated to Australia aboard the emigrant ship Crusader on 15 January 1840 to escape the overpopulation and famine which was raging throughout Ireland.
He arrived in Australia with his family on 10 October 1840, although two young sons died on the journey.