First found in Tuitre (now Antrim), where according to O'Hart, they were Lords of Tuitre. However, the Flynn surname arose independently in several parts of Ireland. Perhaps the oldest line were a Sept of O Floin in Armagh, Ulster, where they were a senior branch of Clanna Rury of Ulidia, claiming descent from King Colla Uais, the famed 4th century Irish King, who in turn was descended from the Heremon royal line.

Ireland became inhospitable for many native Irish Families in the 19th centuries. Poverty, lack of opportunities, high rents, and discrimination forced thousands to leave the island for North America. The largest exodus of Irish settlers occurred with the Great Potato Famine of the late 1840s. For these immigrants the journey to British North America and the United States was long and dangerous and many did not live to see the shores of those new lands. Those who did make it were essential to the development of what would become two of the wealthiest and most powerful nations of the world. These Irish immigrants were not only important for peopling the new settlements and cities, they also provided the manpower needed for the many industrial and agricultural projects so essential to these growing nations. Immigration and passenger lists have documented the arrival of various people bearing the name Flynn to North America: Barnard Flinn who settled in America in 1762; Andrew Flinn settled in New York State in 1803; the Flinns also settled in Georgia, Pennsylvania, Massachusetts, Maryland, and in Canada in 1847.

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