Promoted to rear admiral on 6 January 1888, Hotham became Junior Naval Lord later that month and then went on to be Commander-in-Chief, Pacific Station, with his flag in the armoured cruiser , in February 1890. He sought to intervene in the Chilean Civil War in February 1891 by arranging a peace agreement between the forces of President José Manuel Balmaceda and those of the National Congress of Chile who opposed the President. Unfortunately Hotham was shot at while going ashore, no agreement was signed and the Civil War rumbled on until August 1892 when a much larger international peace-keeping force arrived to restore order. Promoted to vice admiral on 1 September 1893, he was advanced to Knight Commander of the Order of the Bath on 25 May 1895.