Elected a member of the Irish Parliament in 1641, O’Neill appeared to be a supporter of King Charles I. Nevertheless, on 22 Oct 1641, he seized the strategically important Charlemont Castle, Ulster, and then created confusion by claiming that Charles had authorised this act. O’Neill’s followers proceeded to massacre hundreds of England’s colonists in Ulster, but after besieging Drogheda, Co Louth, for several months they were compelled to withdraw (April 1642). This and other failures caused Phelim to lose his command to his kinsman and rival, Owen Roe O’Neill.

After Owen Roe’s death in 1649, Phelim sought unsuccessfully to regain his former position, and he continued to fight bravely until the final defeat of the rebel cause in 1652. The next year he was tried by the English for treason and executed.