Benjamin Vaughan was born in Jamaica to Samuel Vaughan, a British banker and West India merchant planter of Irish Protestant descent, and his Anglo-American wife, Sarah Hallowell, daughter of shipbuilder, Benjamin Hallowell.

He was educated at Newcome’s School and Warrington Academy and attended Trinity Hall, Cambridge, without graduating. He then studied Medicine at the University of Edinburgh. In 1785, during his stay in Edinburgh, he was elected a Fellow of the Royal Society of Edinburgh. His proposers were Allan Maconochie, Lord Meadowbank, Dugald Stewart, and James Hutton.

Vaughan was friends with many of the founding fathers, corresponding with Franklin and Jefferson for many years.