Arundel was the eldest son of Thomas Howard, 4th Duke of Norfolk and Mary Fitzalan, daughter of Henry Fitzalan, 19th Earl of Arundel. He was christened at Whitehall Palace with the royal family in attendance, and was named after his godfather, Philip II of Spain.
His father was attainted and executed in 1572, but Philip Howard succeeded to his mother's heritage upon the death of his grandfather, becoming Earl of Arundel in 1580.
Arundel, and much of his family, became Catholic at a time during the reign of Elizabeth when doing so was politically unwise. While some might be able to do this quietly, Arundel was the premier Earl of England and a cousin of the Queen. He was committed to the Tower of London on April 25, 1585. While charges of treason were never proved, he was to spend ten years in the Tower, until his death of dysentery.
He was attainted in 1589, but his son Thomas eventually had the attainder reversed and succeeded as Earl of Arundel.