Perrot fathered at least four illegitimate children, Sir James Perrot, John Perrot (born c.1565), Elizabeth Perrot, and another daughter whose name is unknown. Sir James Perrot authored the manuscript "The life, deedes and death of Sir John Perrott, knight", published in 1728. John Perrot's name appears in the Inner Temple Register in an entry dated 5 June 1583: "John Perot, of Haryve, Co. Pembroke, 3rd son of John Perot, Knight". Elizabeth, who married Hugh Butler of Pembroke, was the granddaughter of Sir Christopher Hatton, a favourite of Elizabeth I and enemy of Sir John (the source of their hostility being Sir John's relationship with Sir Christopher's unmarried illegitimate daughter, also named Elizabeth).