On 30 September 1856, Johnston married Frances Ellen Palliser at St George's, Hanover Square, London. They had eight sons and two daughters, including Conway Campbell-Johnston (1859–1915), who died with his wife in the sinking of the "Lusitania", and Malcolm Campbell-Johnston, who was Conservative Member of Parliament for East Ham South. Johnston resided in Suffolk, where he was a justice of the peace, and in London.