He was born in Devon and was educated at Merchant Taylors' School and Magdalen College, Oxford, where he was a chorister from 1648 to 1653 and graduated with a B.A.

[1] After 1660, he was assistant to William Spurstow in Hackney, but he conformed after the Act of Uniformity 1662, becoming a lecturer in London.

[2] His written legacy includes his Expositions of the Ten Commandments, which remains in print in the modern era.[when?]

Hopkins married his first wife, Alicia Moore (d.1681), a niece of Sir Robert Viner, sometime Lord Mayor of London, to whom he dedicated his Vanity of the World.

In 1685, at Totteridge, Ezekiel Hopkins married his second wife, Lady Araminta Robartes, the eldest daughter of John Robartes, 1st Earl of Radnor, and his second wife, Isabella, daughter of Sir John Smith.