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 Hieroglyphia (1564) a dense Kaballa influenced work on alchemy. But in 1570 he wrote the preface to the first English translation of Euclid's works.
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 un-noticed for many years in the mineral collection)
He was married three times and had eight children.