Philip was the eldest son of Thomas Howard, 4th duke of Norfolk, executed for high treason in 1572, and of Lady Mary, daughter and heiress of Henry Fitzalan, 12th earl of Arundel. On the death of his maternal grandfather, the 12th earl, in February 1580 he became earl of Arundel.

In 1582 his wife Anne became a Roman Catholic and was committed to the charge of Sir Thomas Shirley by Queen Elizabeth. He was himself suspected of disloyalty and was regarded by the discontented Roman Catholics as the centre of the plots against the Queen's government and even as a possible successor. In 1583 he was with some reason suspected of complicity in Francis Throckmorton (Throckmorton, Francis)'s plot and prepared to escape to Flanders, but his plans were interrupted by a visit from Elizabeth I at his house in London and by her subsequent order to confine himself there. In September 1584 he became a Roman Catholic and made another attempt to leave England. He was then brought before the Star Chamber and sentenced to a fine and imprisonment for life. He was released for a time but was again arrested on a charge of high treason and, in 1589, condemned to death. The sentence was not executed, and he died in the Tower of London. In 1929 he was beatified, and in 1970 he was canonized as one of the Forty Martyrs of England and Wales.