Marcus Herz was born to a poor Jewish family in Berlin in 1747 and was first educated there according to strict Talmudic tradition. In 1766, four years after moving to Königsberg at the age of fifteen to undertake an apprenticeship in business, he matriculated at the “Albertina” as a medical student – its faculty of medicine was the only one in Prussia at the time that would accept Jewish students. As was customary for medical students, Herz began the university with a series of courses in the so-called humaniora (modern languages, philosophy, and mathematics), where he became especially enamored with philosophy as taught to him by Kant. (That Kant had a unique relationship to Herz as well is clear from his decision to have Herz defend his Inaugural Dissertation publicly, a decision that met with some resistance among the faculty.) Because of financial circumstances, Herz left Königsberg to attend medical school first in Berlin and then in Halle, where he received his medical degree in 1774. He then returned to Berlin to practice medicine, where his patients included several high-ranking families, and he, along with his notable wife, Henrietta Herz, maintained a popular salon that functioned as a center for leading young intellectuals such as Wilhelm and Alexander von Humboldt, Friedrich Schleiermacher, and Friedrich Schlegel.

Though he was employed full time as a physician, Herz was able to complete several works in the natural sciences (especially medicine) and philosophy.