In 1844 Muirhead married Katharine Elizabeth, second daughter of Matthew Robinson Boulton. She predeceased her husband in 1890. Six children survived them, the eldest son being Lionel Boulton Campbell Lockhart Muirhead, who composed hymns, and the third son Colonel Herbert Hugh Muirhead, R.E., who played for the Royal Engineers in the 1872 FA Cup Final. Their daughter Beatrix Marion (later Sturt) would write her father's biography, mentioning her brothers but not herself. Lionel's son, Anthony, was MP for Wells in Somerset from 1929 to 1939.