Wöhler, who was born at Eschersheim near Frankfurt, acquired from his father, the master of horse of the crown prince of Hesse-Cassel, an interest in mineralogy – he actually met the aged poet Johann Wolfgang von Goethe, another devotee, in the shop of a Frankfurt mineral dealer. He began training as a physician at Marburg and Heidelberg but was persuaded by Leopold Gmelin to change to chemistry. After a year in Sweden with Jöns Jacob Berzelius he taught chemistry in Berlin and Cassel before his appointment to the chair of chemistry at Göttingen (1836), where he remained for the rest of his life.

Wöhler's most famous discovery occurred in 1828, when he synthesized crystals of urea while evaporating a solution of ammonium cyanate. He wrote excitedly to Berzelius, “I must tell you I can prepare urea without requiring a kidney of an animal, either man or dog.” The significance of his achievement was that urea is an organic substance, which it was hitherto thought could be synthesized only by a living organism. If the constituents of a living body can be put together in the laboratory like common salt or sulfuric acid then there is apparently nothing left to distinguish the living from the nonliving. For this reason Wöhler's work is frequently cited as marking the death of vitalism, although at the time Wöhler was probably more concerned with the chemical reactions involved.

However, it was not seen by Wöhler's contemporaries as having that significance. Just because one substance had been synthesized, no one was prepared to claim that all organic substances could be so created. Justus von Liebig, who knew Wöhler's work well and collaborated with him over a long period of time, was a vitalist and vitalism was too complex and deep-seated an idea to disappear as a result of one experiment. Wöhler's work was more important in opening up whole new dimensions of biochemistry, stimulating work on the chemistry of digestion, respiration, growth, and reproduction.

Wöhler made other contributions to organic chemistry. In 1832, in collaboration with Liebig, he showed that the benzoyl radical (C₆H₅CO) could enter unchanged in a series of compounds: the hydride, chloride, cyanide, and oxide. Thus organic chemistry became, for a time, the chemistry of compound radicals. With the theories of Berzelius, this approach led to a great increase in the knowledge of organic compounds without a corresponding understanding of their chemistry.

In fact organic chemistry became so confusing that Wöhler returned to inorganic chemistry. In later years he tended to concentrate on the chemistry of metals, in particular the production of pure samples of some of the less common metals. He succeeded, at great expense, in obtaining pure aluminum (1827) and beryllium (1828).

With Liebig he was partly responsible for the discovery of isomerism. In 1823, while working in the laboratory of Berzelius, he prepared silver cyanate; at the same time Liebig produced silver fulminate, a compound with very different properties. To their surprise they found both compounds had identical formulas. Berzelius named the phenomenon ‘isomerism’.

One final achievement of Wöhler was the creation of one of the first great teaching laboratories of Europe at Göttingen. From the 1830s nearly all creative chemists of the 19th century spent some time at Göttingen; students came not just from the Continent but also from America and Britain. The tradition persisted until the time of Hitler.