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Ekins was the son of Dr. Jeffery Ekins, dean of Carlisle, and nephew of Dr. John Ekins, dean of Salisbury (1768–1809), and was born presumably at Quainton, Buckinghamshire, where his father was then rector.
He married in 1766 Anne, daughter of Philip Baker of Colston, Wiltshire, and sister of the wife of his brother, John Ekins, dean of Salisbury.