John Hildesley (commonly corrupted to Hilsey) is said to have been a member of the Hildesley family of East Ilsley (previously East Hildesley) on the Berkshire Downs. He was probably a younger son of Edward Hildesley of East Ilsley, in Berkshire and Crowmarsh Gifford in Oxfordshire, just across the river from Wallingford. Traditionally, John became devoted to learning and religion at an early age and he received instructions from a friar of the Dominican house at Bristol, and there he entered this order. From Bristol, he removed himself to the Dominican house at Oxford and, there in May 1527, he graduated as a BD, proceeding to become a DD in 1532. It is probable that he studied also at Cambridge.

By May 1633, Hildesley had become Prior of the Dominican Friary at Bristol, when he wrote a letter to Thomas Cromwell to explain and excuse his conduct in preaching against Hugh Latimer, whose sermons had created great excitement in the city. He seems to have had earlier dealings with Cromwell and apparently regarded him as his patron. In April 1534, Cromwell appointed him provincial of his order and commissioner, along with Dr. George Browne, Provincial of the Augustinians, to visit the friaries throughout England. The commissioners were to administer, to the friars, the oath of allegiance to King Henry VIII, Anne Boleyn and their issue, to obtain from them an acknowledgment of the King as 'Head of the English Church' and to make inventories of their property. The commissioners visited the London houses between 17th and 20th April, went, in May, to such friaries as were within easy reach of London and then proceeded towards the west, Hildesley gaining the nickname of 'the Black Friar of Bristol'. On 21st June, he reported to Cromwell, from Exeter, that, on the whole, the oaths had been taken submissively and, in July, he reached Cardiff in pursuit of two observant friars who were attempting to leave the kingdom. In October, he told Cromwell that he was threatened with the loss of the Provincialship of the Dominicans and complained that Browne was taking it upon himself to assume complete authority. Hildesley's manner of conducting the visitation made him very unpopular and he and Browne were specially denounced by the followers of the 'Pilgrimage of Grace'.

In 1535, on the death of Fisher, Hildesley succeeded him as Bishop of Rochester. According to an entry in Fisher's Register, he was consecrated on 18th September by Archbishop Cranmer at Winchester. On 23rd September, he begged Cromwell for his predecessor's mitre, staff and seal, as being himself too poor to procure such things. In a piteous reply to a complaint from Cromwell that he was "covetous, and not sufficiently complaisant to the King's visitors," he stated that, if Cromwell were not favourable to him, his income would only amount to £200. Cromwell apparently relented because Fisher’s staff is still in possession of Edward Hildesley’s descendants today. In January 1636, Hildesley preached at Queen Catherine's funeral, alleging that, in the hour of death, she had acknowledged that she had never been Queen of England. In March, he obtained a faculty from Cromwell enabling him to remain Prior of the London Black Friars and, when they were dispersed, he received a pension of £60 a year. In 1536, he exercised the duties of censor of the press for the King. On 24th November 1538, he preached at St Paul's Cross and displayed a famous relic, the Holy Blood of Hales Abbey, affirming it to be clarified honey and saffron. On the same day, he similarly denounced the ‘Rood of Grace of Boxley’, exhibiting its machinery and breaking it to pieces. In November 1538, as Perpetual Commendatory of the Black Friars in London, he surrendered the house into the King's hands. His letters, towards the end of his life, complain of sciatica. He died before the end of 1538 and was buried in his cathedral.

Hildesley was occupied, during his last years, in compiling, at Cromwell's order, a service book in English. It appeared in 1539 as 'The Manual of Prayers, or the Primer in English, set out at length, whose contents the reader, by the Prologue next after the Calendar, shall some perceive, and there in shall see briefly the order of the whole book. Set forth by John, late Bishop of Rochester, at the commandment of the right honourable Lord Thomas Cromwell, Lord Privy Seal, Vicegerent to the King’s Highness' (printed by John Mayler for John Waylande). This has a dedication by Hildesley to Cromwell and an elaborate 'instruction of the sacrament', besides some shorter explanatory prologues. Hildesley's arrangement of the Epistles and Gospels is substantially the same as in the later prayer books. The book was republished in great part as 'The Primer both in English and Latin' in 1540. At Cromwell's request Hildesley also prepared 'The Primer in English, most necessary for the Education of Children, abstracted out of the Manual of Prayers, or Primer in Englishe and Latin, set forth by John, late Bishop of Rochester' (1539) and wrote 'De veri Corporis Esu in Sacramento' which was dedicated to Cromwell and is noticed in John White's 'Diacorio Martyrion' (1553). Works also ascribed to Hildesley include 'Resolutions concerning the Sacraments' and 'Resolutions of some Questions relating to Bishops, Priests, and Deacons', but he apparently only assisted the compilation of these documents. He also helped to compile 'The Institution of a Christian Man'.