Born in London. He graduated from St. John's College, Cambridge aged eighteen. He lectured briefly at Cambridge before he left England to study in continental Europe and lecture in Paris and Louvain. He returned to England in the 1540s. In 1553, during the reign of Mary I, he faced a Star Chamber prosecution, accused of black magic, but he was only briefly jailed. When he was released, he became a scientific advisor to Elizabeth I, even deciding on the auspicious date for her coronation in 1558.
Travelling widely abroad with a pension from Elizabeth I, and possibly acting as a spy, Dee strove to increase his knowledge and add to his library. His main published work was Monad Hieroglyphica (1564) a dense Kabbala influenced work on alchemy. But in 1570 he wrote the preface to the first English translation of Euclid's works. He became a close associate of many Elizabethan explorers and entrepreneurs such Sir Humphrey Gilbert.
He met Edward Kelly (or Kelley), a convicted forger, in 1582 and Kelly became his companion. Kelly acted as intermediary for Dee in his attempts to receive visions from 'angels' using a globe of crystal - a magical system and language called Enochian was apparently derived from this scrying. (Dee's crystal globe ended up in the British Museum unnoticed for many years in the mineral collection.) Most of the still existing papers of John Dee are contained within the British Museum, and are available for replication or viewing.
He was married three times and had eight children. His eldest son was Arthur Dee, who was also an alchemist and hermetic author.
The posthumously published account of Dee's encounters with spirits was reprinted in 1974.
In February 1996, Manchester Area Psychogeographic levitated the Corn Exchange in Manchester to commemorate the 400th anniversary of Dr John Dee's arrival in Manchester, as Warden of the Collegiate Church, later the Cathedral.