Succession dispute
O'Brien should have normally succeeded his father on his death on 1 April 1553 as the third earl of Thomond according to English primogeniture. However, at that time O'Brien was only 18; he would have become a ward and the lands would have reverted to the crown until his coming of age. To avoid a wardship, his father appointed O'Brien's uncle Donnell as his tanist (successor) according to Brehon law. His uncle Donnell was formally inaugurated as the O'Brien (chief of the name) and chieftain of the Dal Cais (Dalcassians). He usurped the earldom but was never recognised as earl, whereas O'Brien was counted as the 3rd Earl.
Obliged to surrender Clonroad Castle (near Ennis), the usual residence of his parents, Thomond, as he now was, retreated to Doonmulvihill Castle, on the borders of Galway. Even there he was pursued and besieged by Donnell but relieved by his cousin Thomas Butler, 10th Earl of Ormond.
Subsequently, Donnell petitioned for official recognition as chief of Thomond, and St. Leger, though unable to grant his request, promised to write to Queen Mary in his favour. Matters continued in this uncertain state till the summer of 1558, when the Earl of Sussex, having marched to Limerick with a large army, caused Donnell, Teige and Donough, sons of Murrough, 1st Earl of Thomond, to be proclaimed traitors, and Thomond to be reinstated in his possessions.
Donnell took refuge with Maguire in Fermanagh, and Teige and Donough found a powerful protector in Gerald FitzGerald, 14th Earl of Desmond.