Born about 31 May 1516 in the parish of St Mary Magdalen Old Fish Street, in the City of London, he was the elder brother of Nicholas Harpsfield, the two being sons of John Harpsfield, a gentleman and a mercer, and his wife whose name is unknown.
His paternal grandparents were Nicholas Harpsfield, a Clerk of the Signet, and his wife Agnes Norton.
He was perpetual fellow of New College from 1534 until 1551 and was appointed the first Regius Professor of Greek (Oxford) (approximately 1541-1545).
At some point between 1559 and 1562, he was committed to Fleet Prison, together with his brother Nicholas Harpsfield, for his refusal to swear the Oath of Supremacy.
He wrote letters of appeal to Lord Burghley and Sir Thomas Smith in Greek, as a fellow humanist, and was released on health grounds in 1574.