FitzRoy was promoted to lieutenant on 13 May 1800 into the frigate , Captain the Honourable Henry Blackwood, in which he witnessed the surrender of Malta in September, and took part in the Egyptian Campaign in mid-1801. On 31 October 1801, he was appointed acting-commander and captain of the sloop HMS "Salamine", and after confirmation on 7 January 1802 of his promotion, commanded . He returned to England, and from 26 January 1803 commanded . FitzRoy was promoted to post-captain on 3 March 1804, taking command of the frigate , and was present at the battle of Cape Ortegal on 4 November 1805, and at the invasion of Martinique in February 1809.