Jacob Wilhelm Fockens attended the Agricultural School in Groningen for five years and thereafter studied chemistry, botany and mineralogy for three years at the Academy in Groningen. He continued his studies at Berlin and Goettingen, Germany. The University of Goettingen awarded him the degree Doctor of Natural Science in 1857 for his thesis Ueber die Luftwurzeln der Gewaechse (On the air roots of plants). Returning to the Netherlands he became mayor of Ezinge (in 1859) and later of De Leek (in 1865), both small towns in the province Groningen. During this time he also conducted research in his private laboratory. In 1861 he married Apolonia Elisabeth Oosterhoff. After her death in 1872 he married Aletta Kloek in 1877.
In 1883 Fockens came to the South African Republic (Transvaal) and bought Trevenna Estate, Pretoria, where he started farming. After some time he began teaching natural science at the school of W. Louis in Pretoria. In May 1886 the government appointed him as teacher of mineralogy and around that time he sold Trevenna. In 1895 he requested government to make another room available to him in which to conduct his mineralogy classes. After returning from an overseas journey in 1897 he transferred his classes to the State Gymnasium for boys in Pretoria, which provided teacher training in addition to schooling. He was still teaching mineralogy there in 1898. He became a naturalized citizen of the republic in 1891.
A few years after his arrival Fockens wrote his Beknopt leerboek der delfstofkunde, eene noodzakelijke handleiding voor allen die begerig zijn de delfstoffen der Z.A. Republiek te leeren kennen (Brief textbook of mineral science, an indispensable manual for all who wish to learn about the minerals of the S.A. Republic; Pretoria, 1887). In 1890 he was asked by the government to investigate the dynamite concession which granted Eduard Lippert a monopoly to manufacture and sell dynamite in the Transvaal and which was strongly opposed by the mining industry; however, nothing came of his report. That same year he was asked to report on the need for an agricultural department in the republic. He proposed that district commissioners for agriculture should be appointed, as in the Netherlands; however, his recommendation was disregarded and an agricultural department established. Meanwhile, with funding from the government, he undertook a geological and mineralogical tour from 25 August to 26 September 1890. In December that year he requested authorisation to undertake a second such tour and in May 1892 again wrote to the government about the continuation of his mineralogical journeys.
When the State Museum (later the Transvaal Museum) was created in Pretoria in 1892 Fockens was appointed a member of its Board of Curators and for a year acted as honorary director with Dr H.G. Breyer*. In February 1897 he applied for an appointment as the first director of the museum, but the post went to Dr J.W.B. Gunning*. In 1903, after the Anglo-Boer War (1899-1902) the British authorities repatriated him to the Netherlands.
Fockens should not be confused with his son, W.J. Fockens, born in 1862, who was secretary to the Volksraad of the South African Republic from 1892 to 1899.