He studied geology, botany and zoology at the universities of Berlin and Königsberg, graduating in 1888 with the thesis Untersuchungen über semaeostome und rhizostome Medusen.

In 1892–93 he participated in a Gesellschaft für Erdkunde zu Berlin-sponsored expedition to West Greenland under the leadership of Erich von Drygalski (1865–1949).

From an abundant yield of deep-sea marine fauna collected on the expedition, Vanhöffen was tasked with processing medusa species.

After his return to Germany, he served as a lecturer at the University of Kiel, attaining the title of professor in March 1901.

Led by Erich von Drygalski, the expedition endured periods of hardship due to the "Gauss" being trapped in Antarctic ice for several months.