Harkness entered the army on 13 May 1853 as Ensign in the 55th Regiment, without purchase - on the recommendation of the Duke of Wellington for his grandfather's service. In 1854, he was promoted to lieutenant and served throughout the Crimean Campaign 1854–55. He carried the Queen's colour at the Alma. For heroic conduct, both he and his friend, William Hamilton Richards, were nominated for the Victoria Cross by Major-General Sir Charles Warren. He fought at Inkerman, the assault on the Quarries, the sortie of 26 October 1854, the siege and the fall of Sevastopol and the Battle of the Great Redan. Two pencil drawings of the Crimea War by Harkness survive at the National Army Museum