Flanagan (surname) instance of family name
Origin
Flanagan is just one variation on the original surname which, according to the 19th century writer Reverend Patrick Woulfe, is:
"...the name of at least five distinct families in different parts of Ireland, viz.:
(1) of Fermanagh, a branch of the Oirghialla, who were chiefs of Tuathratha, now anglicised Toorah, an extensive district in the barony of Magheraboy, in the northwest of Co. Fermanagh, and are still numerous in Ulster and the Co. Mayo; 
2) of Roscommon, a branch of the Sil-Murry and of the same stock as the O'Connors, who were hereditary stewards to the kings of Connacht and chiefs of Clann Chathail, a district which embraced several parishes in the neighbourhood of Elphin; 
3) of Westmeath who were anciently lords of Comair and sometimes of all Teffia;
4) of Ely O'Carroll in the present Offaly, who are of the same stock as the O'Carrolls, and were chiefs of Cinel Arga, a district nearly, if not exactly, co-extensive with the present barony of Ballybrit; and
(5) of Waterford, who were formerly chiefs of Uachtartire, now the barony of Upperthird, in the north-west of Co. Waterford, but were dispossessed by the Powers soon after the Anglo-Norman invasion."
Other variations include Flanagin, Flanigan, Flannigan, Flannaghan, Flannagain, Flaniken, Flenigen and so on. The main reason for this variety is the 'Anglicisation' of many Irish place and fore/surnames as a consequence of the colonisation of Ireland (particularly from the 16th century onward) and the subsequent imposition of the English language. With some exceptions all of these variations may be prefixed with Ó (O') - signifying 'son of' or 'Nic' signifying 'daughter of'.
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