He was the eldest son three children born to Eliza Christian Stirling and Sir William John Milliken-Napier, 8th Baronet.
His elder sister was Mary Napier (wife of Robert Speir, of Burnbrae, Renfrewshire and Culdees, Perthshire) and his younger brother was John Stirling Milliken-Napier.
His maternal grandparents were Col. Robert John Milliken-Napier of Culcreuch, Stirling and Anne Campbell.
[3] Upon the death of his father on 4 February 1852, he succeeded to the baronetcy of Merchiston, and became the 9th Baronet.
[2] He was an Honorary Colonel in the 4th Battalion, Princess Louise's Argyll and Sutherland Highlanders.