On 26 April 1808, he married Henrietta Scott Smith (born 1787), the third daughter of the Rev. Dr George Smith (1748–1823), minister of
Galston. They were married at the
manse in Galston. Their thirteen children included the engineer
James Balfour, the physician
George William Balfour and Margaret Isabella Balfour. Margaret married the lighthouse engineer
Thomas Stevenson and was the mother of the author
Robert Louis Stevenson. Their daughter Henrietta Louisa Balfour (1822–1853), married R. H. Traquair, uncle of naturalist and palaeontologist
Ramsay Traquair. Their sons Lewis Balfour (1817–1870) was a merchant in
Calcutta, and Mackintosh Balfour (1825–1894) was a manager in the Bank of Bombay. R. L. Stevenson's book ''
A Child's Garden of Verses'' remembers his summers at Colinton manse. The 1851 census records two grandchildren living at Colinton Manse, Lewis Balfour (born 1842, India, died 1873), and John Boyle (born 1841, India). He died at Colinton manse on 24 April 1860. He was predeceased by his wife Henrietta who also died at the manse on 13 March 1844. Balfour is buried in an open vault on the north side of
Colinton Parish Church, between
James Gillespie and
Admiral John Inglis. ==Family tree==