His mother Adeline Maria Jackson was Julia Stephen's older sister making him a maternal first cousin to Virginia Woolf.
Their surviving daughter was noted physiologist, Dame Janet Vaughan.
Vaughan was educated at Rugby, New College, Oxford and the University of Paris.
Vaughan was an assistant master of Clifton College 1890–1904 before being appointed Headmaster of Giggleswick School (1904–1910), Wellington College (1910–1921) and Rugby School (1921–1931).
He fell and broke his leg while visiting the Taj Mahal in December 1937 during the Indian Science Congress, resulting in his leg being amputated.