Perrot was born between 7 and 11 November 1528, probably at the family seat of Haroldston near Haverfordwest, Pembrokeshire in Wales.
He was the only son of Thomas Perrot (1504/5–1531) and Mary Berkeley (c.1511–c.1586), the daughter of James Berkeley (died c.1515) of Thornbury, Gloucestershire.
He had two sisters: Jane, who married Sir John Philipps of Picton Castle; and Elizabeth, who married John Price of Gogerddan.

Perrot resembled Henry VIII in temperament and physical appearance, and it was widely believed that he was the bastard son of the late King.
The main source for this belief was Sir Robert Naunton (husband of Perrot's granddaughter, Penelope), who had never known Perrot and used second-hand accounts to make his case.
The case is weakened by the fact that Perrot was Mary Berkeley's third child, not her first, and that she and the King are not recorded to have been in the same place at the crucial time.
Naunton claimed that Sir Owen Hopton, Lieutenant of the Tower of London, overheard Perrot say, "Will the Queen suffer her brother to be offered up as a sacrifice to the envy of his frisking adversaries?",
suggesting that Perrot himself asserted his royal paternity.
However, Hopton had been removed from office by the Queen eighteen months prior to Perrot's imprisonment, so he could not have overheard Perrot make the claim there.

Perrot joined the household of William Paulet, 1st Marquess of Winchester, and thereby gained his introduction to Henry VIII.
His advancement faltered on the death of the King in January 1547, but in the following month he was knighted at the coronation of Henry's successor, Edward VI.

In 1551 Perrot was appointed High Sheriff of Pembrokeshire, and in June of the same year he visited France in the train of William Parr, 1st Marquess of Northampton, who had been sent to arrange Edward VI's betrothal to Elisabeth of Valois, the infant daughter of Henry II of France.
Perrot's skill as a knight and in the hunt fascinated King Henry, who sought to retain him for reward.
Perrot declined, but on his return to England his debts were paid by the French Crown.

During the reign of Mary I Perrot suffered a brief imprisonment in the Fleet with his uncle, Robert Perrot, on a charge of sheltering heretics at his house in Wales.
Following his release he declined to assist the Earl of Pembroke in seeking out heretics in south Wales, but in 1557 was content to serve the same Earl at the capture of Saint-Quentin in France.

Perrot inherited the castle and lordship of Carew.
At the beginning of Elizabeth I's reign the naval defence of South Wales was entrusted to his care.
His advancement continued in 1562, when he was elected Knight of Pembrokeshire.
He served as member of parliament for Carmarthenshire in 1547, Sandwich in 1553 and 1555, Wareham in 1559 (presumably through pressure exerted on the Rogers family by the 2nd Earl of Bedford, his former commander), Pembrokeshire in 1563, and Haverfordwest in 1589.
Perrot was born between 7 and 11 November 1528, probably at the family seat of Haroldston near Haverfordwest, Pembrokeshire in Wales. He was the only son of Thomas Perrot (1504/5–1531) and Mary Berkeley (c.1511–c.1586), the daughter of James Berkeley (died c.1515) of Thornbury, Gloucestershire. He had two sisters: Jane, who married Sir John Philipps of Picton Castle; and Elizabeth, who married John Price of Gogerddan.
Perrot resembled Henry VIII in temperament and physical appearance, and it was widely believed that he was the bastard son of the late King. The main source for this belief was Sir Robert Naunton (husband of Perrot's granddaughter, Penelope), who had never known Perrot and used second-hand accounts to make his case. The case is weakened by the fact that Perrot was Mary Berkeley's third child, not her first, and that she and the King are not recorded to have been in the same place at the crucial time. Naunton claimed that Sir Owen Hopton, Lieutenant of the Tower of London, overheard Perrot say, "Will the Queen suffer her brother to be offered up as a sacrifice to the envy of his frisking adversaries?", suggesting that Perrot himself asserted his royal paternity. However, Hopton had been removed from office by the Queen eighteen months prior to Perrot's imprisonment, so he could not have overheard Perrot make the claim there.
Perrot joined the household of William Paulet, 1st Marquess of Winchester, and thereby gained his introduction to Henry VIII. His advancement faltered on the death of the King in January 1547, but in the following month he was knighted at the coronation of Henry's successor, Edward VI.
In 1551 Perrot was appointed High Sheriff of Pembrokeshire, and in June of the same year he visited France in the train of William Parr, 1st Marquess of Northampton, who had been sent to arrange Edward VI's betrothal to Elisabeth of Valois, the infant daughter of Henry II of France. Perrot's skill as a knight and in the hunt fascinated King Henry, who sought to retain him for reward. Perrot declined, but on his return to England his debts were paid by the French Crown.
During the reign of Mary I Perrot suffered a brief imprisonment in the Fleet with his uncle, Robert Perrot, on a charge of sheltering heretics at his house in Wales. Following his release he declined to assist the Earl of Pembroke in seeking out heretics in south Wales, but in 1557 was content to serve the same Earl at the capture of Saint-Quentin in France.
Perrot inherited the castle and lordship of Carew. At the beginning of Elizabeth I's reign the naval defence of South Wales was entrusted to his care. His advancement continued in 1562, when he was elected Knight of Pembrokeshire. He served as member of parliament for Carmarthenshire in 1547, Sandwich in 1553 and 1555, Wareham in 1559 (presumably through pressure exerted on the Rogers family by the 2nd Earl of Bedford, his former commander), Pembrokeshire in 1563, and Haverfordwest in 1589.
John Perrot