In 1903, Chancellor married Mary Elizabeth Howard (1881–1976), daughter of George Rodie Thompson, DL, JP, of Lynwood, Ascot, Berkshire. They had three children: Christopher John Howard Chancellor (1904–1989), who married Sylvia Mary Paget in 1926; Robert Duff (Robin) Chancellor (1921-2010); and a daughter, Elizabeth Rosemary Alice Chancellor (1906–1971), known as Rosemary, who married Air Chief Marshall William Elliot in 1931. Christopher and Sylvia had two children: John Paget Chancellor and Alexander Chancellor; Rosemary and William also had two children: Louise Elliot (Halsey) and Simon Elliot.
