In 1559 FitzWilliam was appointed Vice-Treasurer of Ireland and elected a member of the Irish House of Commons to represent Co Carlow. His conduct as treasurer provoked allegations of corruption against him and, although these were never proven, they dogged him throughout his career. Between 1559 and 1571 he served five times as Lord Justice of Ireland (during the absences of the Earl of Sussex, and of his successor, Sir Henry Sidney). In 1571 he was appointed to the office of Lord Deputy itself, but like Queen Elizabeth's other servants he received scant and infrequent allotments from the Treasury. His government was thus marked by penury and its attendant evils, inefficiency, mutiny and general lawlessness.