MacGregor was born on 31 March 1842, the third son of Sir John Athol Bannatyne Murray MacGregor, 3rd Baronet, and his wife Mary Hardy, daughter of Vice-Admiral Sir Thomas Masterman Hardy, 1st Baronet.
In 1884 he was married to Annie Louise Middleton, daughter of Colonel William Alexander Middleton CB; they had one daughter, Eva Mary McGregor (1886–1964), who died unmarried.
He lived at Aynsome, Cartmel, Lancashire, and was a member of the Caledonian Club; he also served as a Justice of the Peace.
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