He was the only son of John Wharton (d. 10 June 1629) by his wife Elizabeth, daughter of Roger Hodson (d. 10 March 1646) of Fountains Abbey, and was born at Winston-on-Tees, county Durham, on 31 August 1614.

When, however, a vacancy occurred and he applied for the fulfilment of the promise, he was put off with a grant of honourable augmentation to his paternal arms, for which he had to pay Sir William Dugdale.

He wrote four English verses under a fanciful engraving prefixed to a translation by Elias Ashmole, entitled Arcanum, or the Grand Secret of Hermetic Philosophy, and published in his Theatrum Chemicum Britannicum (London, 1652).

[2] Ashmole and Wharton worked together on the catalogue of the Musaeum Tradescantianum, printed in 1650, stemming from a visit they paid John Tradescant the younger in 1650.

Wharton published Adenographia; sive glandularum totius corporis descriptio, London, 1656 (plates); Amsterdam, 1659; Oberwesel, 1664, 1671,1675; Düsseldorf, 1730.