He was born in London, Canada West on May 13, 1843, the son of Captain William Mackintosh, of Wicklow, Ireland, an Irish-born officer posted to Canada with the British Army's Ordnance Department, who later served as County Engineer for Middlesex County, Ontario. Mackintosh's paternal grandfather was Captain Duncan Mackintosh, a Scotsman who had been sent to Ireland with the British Army's Highland regiment during the Irish Rebellion of 1798.