In 1878 he acted as architect of the Indian section and commercial agent to the Indian government at the Paris Exhibition. In 1880 Clarke arranged the Indian collections at South Kensington, which led to taking on the position of special commissioner in India and then becoming keeper of the India Museum at South Kensington in 1883. His acquisitions included the Hamzanama folios, early Mughal illustrations of the epic adventures of Hamza by northern Indian and Iranian artists. He also bought contemporary crafts, architectural woodwork and drawings. In 1892 Clarke was appointed Keeper of the art collections, in 1893 promoted to Assistant Director before finally becoming Director in 1896. During his time as Director he also filled the posts of Royal Commissioner at the 1900 Paris Exhibition and at St Louis in 1904. He resigned from the South Kensington Museum (renamed in 1899 as the Victoria and Albert Museum) in 1905.