Born at Graffham, in Huntingdonshire, England to a long line of clergymen.  His father, grandfather and great-grandfather had all been in the ministry.

At the age of fifteen he was apprenticed to Thomas Parkhurst, bookseller, at the sign of the Bible and Three Crowns, Cheapside, London.  Dunton ran away at once, but was soon brought back and began to love books.

During the struggle which led to the Glorious Revolution of 1688, Dunton was the treasurer of the Whig apprentices. He became a bookseller at the sign of the Raven, near the Royal Exchange, and married Elizabeth Annesley, whose sister married Samuel Wesley. His wife managed his business, so that he was left free in a great measure to follow his own eccentric devices.

In 1686, probably because he was concerned in the Monmouth Rebellion, he visited New England, where he stayed eight months selling books and observing with interest the new country and its inhabitants. Dunton had become security for his brother's debts, and to escape the creditors he made a short excursion to Holland. On his return to England, he opened a new shop in the Poultry in the hope of better times. Here he published weekly the Athenian Mercury which professed to answer all questions on history, philosophy, love, marriage and things in general. His wife died in 1697, and he married a second time; but a quarrel about property led to a separation; and being incapable of managing his own affairs, he spent the last years of his life in great poverty.

He wrote a great many books and a number of political squibs on the Whig side, but only his Life and Errors of John Dunton (1705), on account of its naiveté, its pictures of bygone times, and of the literary history of the period, is remembered. His letters from New England were published in America in 1867.