He was born at Küblingen (now a part of Schöppenstedt, Lower Saxony). He studied theology at the University of Helmstedt, where he was a pupil of Heinrich Philipp Konrad Henke. From 1795 to 1805, he worked as a tutor to the family of a wealthy Hamburg merchant. In 1805 he was repentant at the University of Göttingen with a dissertation titled Graecorum mysteriis religioni non obtrudendis, he then served as a professor of theology at the University of Rinteln (1806–1810), and at the University of Halle from 1810 onwards.
Wegscheider was a leading figure of dogmatic theological rationalism — for instance, he considered supernatural revelation to be an impossibility. Because of his rationalist teachings, he, along with his colleague Wilhelm Gesenius, were attacked by followers of Supernaturalism, creating a situation that led to a government investigation (1830). Ultimately, he retained his office at Halle, but lost his former influence.