John Allen, a son of Chief Justice William Allen, was born and died in Philadelphia. After attending the Academy and College of Philadelphia (now the University of Pennsylvania), John Allen finished his legal studies at the Temple in London. He was elected a member of the American Philosophic Society in 1768. At the beginning of the Revolution he was a common councilman in Philadelphia.
When he opposed independence, Allen was summoned to a trial for high treason by Act of the Pennsylvania Assembly. In December 1776, Allen put himself under the protection of British General Howe.
Allen was a trustee of the College of Philadelphia from 1769 until his 1778 death in Philadelphia. He served as treasurer of the board in 1769.