Burnet was born at Croft and was educated at Cambridge University, becoming a fellow of Christ's College in 1657. After a period as tutor to various noblemen he was appointed master of Charterhouse School in 1685. He was also appointed chaplain to William III in 1686 but was later forced to resign (1692) because of his controversial account of the history of the Earth.

In 1681 he published his Telluris theoria sacra, which was published in an English version as The Sacred Theory of the Earth in 1684 and revised and extended in 1691. In this he tackled the problem that was to face all geologists until this century – how to write a history of the Earth that was consistent with the account given in Genesis. His aim was to take the facts of scripture and show how they could be used to give a rational account of the development of the Earth.

His theory was that the Earth had once been entirely smooth, trapping beneath its shell a large volume of water. Owing to the action of the Sun this shell – the Earth's crust – cracked and released the flood of water; parts of the shattered crust remaining formed the mountains.

Burnet's attempt to explain the history of the Earth in natural terms met a torrent of opposition, both theological and scientific. The strongest argument against this explanation was the presence of marine fossils in mountains for, if the Earth's crust from which the mountains were formed was created before the flood, how could it have come to contain evidence of marine life?