Lieutenant (later Captain) Henry Clerk of the Royal Artillery was appointed as additional officer (to Lieutenant Frederick Eardley-Wilmot*) at the Magnetic Observatory that had been established in the grounds of the Royal Observatory, Cape of Good Hope, by Eardley-Wilmot in March 1840. Clerk arrived at the Cape in December 1844 and assisted with the magnetic observations. For most of 1843 he was in charge of the observatory while Eardley-Wilmot was on leave.
In January 1844 Clerk sailed on HM bark Pagoda deep into the Southern Ocean, along the shores of Antarctica, to carry out a magnetic survey of that portion of the southern hemisphere not included in the survey carried out by Sir James Ross's expedition. He was assisted by Lieutenant T.E.L. Moore. The survey was made by direction of the Lords Commissioners of the Admiralty at the request of the Royal Society. Clerk published a paper based on the voyage, "Meteorological observations made on board H.M. (hired) Bark Pagoda from January 10 to June 20, 1845, between 20º and 68º South latitude and 0º-120º East longitude", which was published in the Transactions of the American Philosophical Society (1846, pp. 433-440). On the way back, from Port Natal (Durban) to Simon's Bay during 12 to 23 June 1845, he made observations of the magnetic declination. His observations, which were published in the South African Commercial Advertiser in July, showed that the variation of the compass increased gradually from just over 25ºW at Port Natal, to just over 29ºW in Simon's Bay. In the same issue of the newspaper he gave notice that he was about to leave the Cape Colony.