He studied metaphysics at the Universities of Rostock and Giessen, where he in 1608 he earned his degree. From 1609 to 1614 he was a professor of mathematics at the University of Giessen, and in 1614–15 was involved with studies of educational reform with Wolfgang Ratke (1571–1635) and Christoph Helvig (1581–1617). In 1616 he returned to Rostock to study medicine, and in 1619 received his medical doctorate from the University of Padua. Afterwards he practiced medicine in Lübeck from 1619 to 1623. In 1622 at Rostock, he founded an early scientific society known as Societas Ereunetica sive Zetetica
From 1624 to 1628 Jungius was a professor of mathematics at Rostock, which was briefly interrupted in 1625 when he spent time as professor of medicine at the University of Helmstedt. From 1629 until 1657 he was professor of natural sciences at the Akademisches Gymnasium, a secondary school in Hamburg. Jungius believed that science was based on mathematics, and at Hamburg stressed the importance of critical thinking to his students. He also felt that mathematics and logic served as a remedy to metaphysical and mystical speculation.
Jungius was an important figure of 17th century atomism, and was an advocate of a "corpuscular chemistry" that assumed the conservation of mass. He also demonstrated that a catenary was not a parabola, which was contrary to Galileo's assumption that it was. In 1638 he published the textbook Logica Hamburgensis, which presented late medieval theories and techniques of logic. Here he demonstrated oblique cases of arguments that did not adhere to simpler forms of inference; An example being: "The square of an even number is even; 6 is even; therefore, the square of 6 is even".
Gottfried Wilhelm Leibniz wrote, "While Jungius of Lübeck is a man little known even in Germany itself, he was clearly of such judiciousness and such capacity of mind that I know of no other mortal, including even Descartes himself, from whom we could better have expected a great restoration of the sciences, had Jungius been either known or assisted.