Marriage and children
After the war, Clarke returned to Australia; in 1947 married Kathleen Grant Hay, the daughter of successful Melbourne brewery owner, Peter Grant Hay. The couple had three children:
Rupert Grant Alexander Clarke (b. 12 December 1947), who married Susannah Law-Smith, daughter of Sir Robert Law-Smith in 1978. At the time of the engagement, Susannah was employed as Private Secretary to the-then Wife of the Prime Minister of Australia Tamie Fraser. Rupert succeeded his father as the Clarke Baronet of Rupertswood in 2005.
Samantha Kathleen Clarke (b. 1980)
Rupert Robert William Clarke (b. 1981)
Joanna Georgina Clarke (b. 1983)
Vanessa Margaret Clarke (b. 1952), who married Roden Cutler, son of New South Wales Governor Lt. Gen. Sir Arthur Roden Cutler V.C. in 1975, with whom she has four children.
Peter Robert Justin John Clarke (b. 1955), who married Andrea Pitt in 1983.
Alexandra Kathleen Grant (b. 1984)
William Peter Norman Grant Clarke (b. 1986)
Lady Clarke died in 1999, and in the following year Sir Rupert remarried to Gillian de Zoete.
Following his father's death in 1926, Rupert inherited the 4,622-acre Bolinda Vale estate in the Shire of Romsey, north of Melbourne, as well as £150,000 in Trust funds which would vest into his ownership on his 21st birthday. He also inherited a reversionary right to his father's residuary estate jointly with his brother, sister and two half-sisters, subject to his mother's life interest in this property under the terms of his father's will.
In 1962 his wife Kathleen, Lady Clarke purchased the historic Pateley House located at 56 Avoca Street, South Yarra for £25,000, which had been constructed in 1859. Sir Rupert and Lady Clarke renamed the property Richmond House in acknowledgement of Lady Clarke's father's business interests, and Richmond House served as the family's town residence in Melbourne for the remainder of the 20th century. Following Lady Clarke's death in 1999, Richmond House was sold to Melbourne stockbroker Michael Kirwan for $3.7 million.