Perrot was born about 1527 in Haroldston, Pembrokeshire, Wales. He was the son of Mary Berkley, who afterwards married Thomas Perrot, a Pembrokeshire gentleman. He was generally reputed to be a son of Henry VIII, and was attached to the household of William Paulet, 1st marquess of Winchester.
Sir John was educated at St David's, Pembrokeshire.
At the age of eighteen he was placed in the household of William Paule, first Marquis of Winchester. He was introduced to Court in the autumn of 1549 and was knighted at the coronation of Edward VI.
During Mary's reign he suffered a short imprisonment on the charge of harbouring his uncle, Robert Perrot, and other heretics.
In spite of his Protestantism he received the castle and lordship of Carew in Pembrokeshire, and at the beginning of Elizabeth's reign he was entrusted with the naval defence of South Wales.
In 1570 Perrot reluctantly accepted the newly created post of lord president of Munster. He landed at Waterford in February of the next year, and energetically set about the reduction of the province. In the course of two years he hunted down James Fitzmaurice Fitzgerald, whose submission he received in 1572.
Perrot resented the reinstatement of Gerald Fitzgerald, 15th earl of Desmond, and after vainly seeking his own recall left Ireland without leave in July 1573, and presenting himself at court was allowed to resign his office, in which he was succeeded by Sir William Drury.
He returned to his Welsh home, where he was fully occupied with his duties as vice-admiral of the Welsh seas and a member of the council of the marches. Although in 1578 he was accused by the deputy-admiral, Richard Vaughan, of tyranny, subversion of justice and of dealings with the pirates, he evidently retained the royal confidence, for he was made commissioner for piracy in Pembrokeshire in 1578, and in the next year was put in command of a squadron charged to intercept Spanish ships on the Irish coast.
The recall of Arthur Grey, Lord Grey de Wilton, in 1582, left vacant the office of lord deputy of Ireland, and Perrot was appointed to it early in 1584. Sir John Norris became lord president of Munster and Sir Richard Bingham went to Connaught. Perrot's chief instructions concerned the plantation of Munster, where the confiscated estates, some 600, 000 acres in extent, of the earl of Desmond were to be given to English landlords at a nominal rent, provided that they brought with them English farmers and labourers.
Before he had had time to embark on this enterprise he heard that the Highland clans of Maclean and MacDonnell were raiding Ulster at the invitation of Sorley Boy MacDonnell, the Scoto-Irish constable of Dunluce Castle. He marched into Ulster, but Sorley Boy escaped him, and crossed to Scotland, only to return later with reinforcements. The lord deputy was roundly abused by Elizabeth for undertaking “a rash, unadvised journey, ” but Sorley Boy was reduced to submission in 1586.
In 1585 Perrot succeeded in completing the “composition of Connaught, ” a scheme for a contract between Elizabeth and the landholders of the province by which the queen should receive a small quitrent.
During his career as lord deputy he had established peace, and had deserved well of Elizabeth. But a rash and violent temper, coupled with unsparing criticism, not to say abuse, of his associates, had made him numerous enemies. A hastily conceived plan for the conversion of the revenues of St Patrick's Cathedral, Dublin, to provide funds for the erection of two colleges, led to a violent quarrel with Adam Loftus, archbishop of Armagh. Perrot had interfered in Bingham's government of Connaught, and in May 1587 he actually struck Sir Nicholas Bagenal, the knight marshal, in the council chamber. Elizabeth decided to supersede him in January 1588, but it was only six months later that his successor, Sir William Fitzwilliam, arrived in Dublin. After his return to England his enemies continued to work for his ruin, and a forged letter purporting to be from him to Philip II. of Spain gave colour to an accusation of treasonable correspondence with the queen's enemies, but when he was tried before a special commission in 1592 the charge of high treason was chiefly based on his alleged contemptuous remarks about Elizabeth.
He was found guilty, but died in the Tower in September 1592. Elizabeth was said to have intended his pardon.
After Edward's death and the ascendance of Mary I to the throne, Sir John was denounced as a Protestant.
Perrot married firstly Anne Cheyne, by whom he had a son and heir, Sir Thomas Perrot. After the death of his first wife Perrot remained unmarried for a decade. In 1563 or 1564 he married Jane Prust. She had a son and two daughters by Perrot. Perrot fathered at least four illegitimate children.
