Vaughan was elected to the American Philosophical Society in 1784, became treasurer in 1791 and librarian in 1803, and served in these posts until his death. Vaughan was instrumental in building the Society's library collection and in introducing scientists and historians to each other through his letters and Sunday breakfasts. Although not a scholar himself, he appreciated the talents and contributions of his scholarly colleagues.
John Vaughan and Thomas Jefferson maintained an on-going correspondence for more than thirty years. The business-oriented letters focus primarily on activities of the American Philosophical Society and on personal financial transactions.