He married Lucy Marianne Vaughan Morgan (1871–1941), daughter of Octavius Vaughan Morgan (1837–1896), and granddaughter of Thomas Morgan of Pipton, near Glasbury, Breconshire (1796–1847). Their daughter Joyce Morgan Brunner married Sir William Worsley, 4th Baronet, and their granddaughter Katharine married Prince Edward, Duke of Kent, thereby becoming Her Royal Highness The Duchess of Kent. Their son Felix succeeded as the 3rd baronet upon the death of Sir John, age 63.
