In August 1899 Fuller was appointed as the first Government Entomologist of Natal, stationed in Pietermaritzburg. Soon after his arrival he improved the crude methods used in Natal to poison locusts, and convinced the government of the colony to organize systematic campaigns to destroy the insects. The success of these efforts led to the introduction of similar campaigns in other parts of the country. His first and second Report of the Government Entomologist (1899/1900, 1901) included descriptions of many insect pests and plant diseases which, if combined into a single volume, would have made a good handbook for agriculturalists. In addition he published almost 100 articles, notes and letters dealing with insect pests and their treatment or prevention, as well as other agricultural matters, in the Natal Agricultural Journal between 1899 and 1910. During the next few years he continued his articles in the Agricultural Journal of the Union of South Africa. Other contributions were published by the Natal Department of Agriculture. One of his investigations was into the export of fruit (particularly pineapples) to Britain and in 1906 he published A fruitgrower's handbook of the culture and management of fruit trees. Among his assistants during his years in Natal were H. von P. Berensberg* and Albert Kelly*. By 1909 he was a member of the Board of Trustees of the Natal Museum.

In April 1912 Fuller was appointed Assistant Chief of the Division of Entomology in the Department of Agriculture of the Union of South Africa in Pretoria. His studies of the anatomy, habits and biology of termites and their economic importance and control led to significant advances in knowledge. His first papers on termites, "White ants in Natal" (published by the Union Department of Agriculture) and "White ants in buildings, orchards and plantations" (Agricultural Journal of the Union of South Africa) appeared in 1912. In 1915 he published a paper on "Termite economy" in the Report of the South African Association for the Advancement of Science, and "Observations on some South African termites" in the Annals of the Natal Museum. Further "Notes on white ants" appeared in the first two Bulletins of the South African Biological Society in 1918. In order to place the classification of this group on a sounder basis he made a special study of their wing venation, respiratory system, development of the antennae and the structure of the thorax and abdomen of certain species. The results were published in the Annals of the Natal Museum in 1919 and 1920, and in Entomology Memoir No. 2 of the Department of Agriculture in 1924. In several systematic papers on South African termites in the South African Journal of Natural History during 1921, 1922 and 1925 he described a large number of new species. However, most of the names he allocated later became synonyms.

Later in his career Fuller developed a particular interest in the tsetse fly and in 1923 published Tsetse in the Transvaal and surrounding territories, an historical review as Entomology Memoir No. 1 of the Department of Agriculture. The study had originally been written up for the combined ninth and tenth Reports of the Director of Veterinary Education and Research, published in 1924. It was based on his study of the reports of early travellers in the region, combined with field work to establish their exact routes, and dealt with the early occurrence and later disappearance of tsetse in northern and eastern Transvaal. An important early source of information was the diary of the Voortrekker Louis Trichardt. Fuller's historical research into Trichardt's trek was published after his death in a richly illustrated book, Louis Trichard's trek across the Drakensberg, 1837-1838 (Van Riebeeck Society, Series 1, No. 13, 1932).

Fuller collected many fungi, and the plant species Hyobanche fulleri (Fam. Scrophulariaceae) was named in his honour by E.P. Phillips*.

He was a member of the United States Association of Economic Entomologists; also a founding member of the South African Biological Society, serving on its editorial committee and as its honorary secretary in 1918, and as Editor-in-Chief of its South African Journal of Natural History from 1919 to 1927. In 1919 he was awarded the society's Captain Scott Memorial Medal. He was promoted to Head of the Division of Entomology early in 1927, but in October that year retired on pension at the age of 55. In February 1928 he became chief entomologist of Mozambique, but died as a result of injuries sustained in a motor accident later that same year.

Fuller's research was characterized by thoroughness and attention to detail. He wrote in an excellent literary style and used his artistic abilities to produce illustrations for his papers. In recognition of his contributions to science the University of South Africa awarded him an honorary Doctor of Science (DSc) degree in 1928. He and his wife Ethel May Frederica Fuller had two daughters.