John J. Cleverly was educated in Portsmouth, England, and came to the Cape Colony at the age of eighteen. He joined the civil service of the Cape Colony in October 1876 as a clerk in the railway construction service. In November 1878 he became acting fourth examining customs officer at East London, rising to second examining officer by 1883. In September 1884 he was transferred to Port Elizabeth as second clerk in customs, acting for some time as chief clerk and warehouse keeper. He wrote a short treatise, The consolidation of the British Empire, which was published in Port Elizabeth in 1887 and in which he advocated a federation of Great Britain and its colonies. In July 1889 he was transferred to Walfish Bay as acting resident magistrate and customs officer. His appointment as resident magistrate was confirmed in July 1890. In addition to his duties as magistrate he had diplomatic contacts with the German administration of German South West Africa (now Namibia) and supervised the construction of some public works such as the railway and jetty.
At this time Walfish Bay was a desolate outpost and none of the magistrates that preceded him had been able to cope with the trying conditions. There was but a small and isolated European community, with no medical facilities; fresh produce was scarce, and drinking water had to be brought in by ships from the Cape. However, Clevely gave good service for many years. In his spare time he collected marine algae and became a liberal contributor to the Cape Government Herbarium via Government Botanist P. MacOwan*. Among others he provided several large specimens of Welwitschia mirabilis, the largest of which was sent to the Chicago World Fair in 1892. In 1891 he sent MacOwan a note titled "The 'Nara' (Acanthosicyos horrida Welw.)", which was eventually published in Kew Bulletin in 1903. He also sent ants to the South African Museum from Walfish Bay in 1891.
In February 1893 the German warship Falke anchored in Walfish Bay. Its crew had just removed the padrao (stone cross) erected on Cape Cross by Diogo Cao* in 1486. Cleverly inspected the cross and recorded the incident in his journal.
From 1899 he manned a second order meteorological station in Walfish Bay for the Cape of Good Hope Meteorological Committee, taking a series of five observations per day. His observations for 1899 were intermittent, and the station was not in operation during 1901 and 1902, as Cleverly had been transferred to East London from 1 June 1901. There he was collector of customs and registrar of shipping. He returned to Walfish Bay as civil commissioner and resident magistrate in May 1903, and during that year F.H. Guthrie and he manned a third order or climatological station there. This was again upgraded to a second order station from the beginning of 1904, with Cleverly as observer. Responsibility for the work was taken over by G. Gale in the course of 1905, when Cleverly left the civil service of the Cape Colony. He died the next year.