Issue
By his second wife, Catherine Fenton, daughter of Sir Geoffrey Fenton and his wife Alice Weston, the 1st Earl of Cork had fifteen children:
Roger Boyle (1 August 1606, Youghal, County Cork, Ireland–10 October 1615, Deptford, Kent, England, where he was buried).
Lady Alice Boyle (1607–1667), married David Barry, 1st Earl of Barrymore, then after his death, married John Barry, of Liscarroll, co Cork, Ireland.
Lady Sarah Boyle (1609–1633), married Sir Thomas Moore, then after his death married Robert Digby, 1st Baron Digby.
Lady Lettice Boyle (1610–1657), married Colonel George Goring, Lord Goring.
Lady Joan Boyle (1611–1657), married George FitzGerald, 16th Earl of Kildare ("the Fairy Earl").
Richard Boyle, 2nd Earl of Cork and 1st Earl of Burlington (1612–1698), Lord High Treasurer of Ireland (1660–1695).
Lady Katherine Boyle (1615–1691), married Arthur Jones, 2nd Viscount Ranelagh.
Hon. Geoffrey Boyle
Lady Dorothy Boyle, married Sir Arthur Loftus of Rathfarnham and was the mother of Adam Loftus, 1st Viscount Lisburne.
Lewis Boyle, 1st Viscount Boyle of Kinalmeaky (1619–1642), succeeded under special remainder by his older brother Richard.
Roger Boyle, 1st Earl of Orrery (1621–1679)
Francis Boyle, 1st Viscount Shannon
Lady Mary Boyle, married Charles Rich, 4th Earl of Warwick.
Hon. Robert Boyle (1627–1691), author of The Sceptical Chymist; considered to be the father of modern chemistry.
Lady Margaret Boyle
Boyle erected an elaborate monument to himself, his wives, his mother, and his children in The Collegiate Church of St Mary Youghal, County Cork and there is a similar but much larger Boyle monument in St Patrick's Cathedral, Dublin. His elder brother John is also buried in the tomb.