Kekule was born into an upper-middle-class family of civil servants and as a schoolboy demonstrated an aptitude for art and languages, as well as science subjects. Intending to be an architect, he entered the nearby University of Giessen, but soon he was “seduced” (as he later expressed it) to the study of chemistry by the attractive teaching of Justus Liebig (Liebig, Justus, Freiherr von).

Kekule received a doctorate in 1852, but no teaching positions were immediately available, so he continued with postdoctoral work in Paris, Chur (Switzerland), and London. In Paris he formed friendships with Charles Gerhardt (Gerhardt, Charles), from whose “type” theory of organic composition Kekule began to develop his own ideas, and with the important chemical theorist Charles-Adolphe Wurtz (Wurtz, Charles-Adolphe). In London he was particularly influenced by Alexander Williamson (Williamson, Alexander William), who had recently begun to expand this type theory into what became an incipient understanding of atomic valence.

Early in 1856 Kekule moved to the University of Heidelberg, where he qualified as a lecturer and began to produce important research in organic chemistry. He had a prodigious memory for chemical details, a complete mastery of English and French in addition to his native German, and—most important—one of the most fruitful scientific imaginations of any scientist of his day. He was also energetic, intense, and a superb teacher. In 1858 he was called to the University of Ghent in Belgium, where he taught chemistry in French. Nine years later he was hired as a full professor and chairman of the chemistry department at the University of Bonn, where he took charge of a large new laboratory and where he remained for the rest of his career.

Kekule's most important single contribution was his structural theory of organic composition, outlined in two articles published in 1857 and 1858 and treated in great detail in the pages of his extraordinarily popular Lehrbuch der organischen Chemie (“Textbook of Organic Chemistry”), the first installment of which appeared in 1859 and gradually extended to four volumes. Kekule argued that tetravalent carbon atoms could link together to form what he called a “carbon chain” or a “carbon skeleton,” to which other atoms with other valences (such as hydrogen, oxygen, nitrogen, and chlorine) could join. He was convinced that it was possible for the chemist to specify this detailed molecular architecture for at least the simpler organic compounds known in his day. Kekule was not the only chemist to make such claims in this era. The Scottish chemist Archibald Scott Couper (Couper, Archibald Scott) published a substantially similar theory nearly simultaneously, and the Russian chemist Aleksandr Butlerov (Butlerov, Aleksandr) did much to clarify and expand structure theory. However, it was predominantly Kekule's ideas that prevailed in the chemical community.

Kekule is also famous for having clarified the nature of aromatic compounds (aromatic compound), which are compounds based on the benzene molecule. Kekule's novel proposal for a cyclic benzene structure (1865) was much contested but was never replaced by a superior theory. This theory provided the scientific basis for the dramatic expansion of the German chemical industry in the last third of the 19th century. Today, the large majority of known organic compounds are aromatic, and all of them contain at least one hexagonal benzene ring of the sort that Kekule advocated.

In addition to his theoretical contributions, Kekule produced a large volume of original experimental work that considerably widened the scope of organic chemistry. His studies of unsaturated compounds, organic diacids, and aromatic derivatives were particularly noteworthy. He also led a significant research group, consisting of advanced students, postdoctoral workers, and junior colleagues, at both Ghent and Bonn. After the death of Liebig, Kekule was invited to succeed him at the University of Munich, but Kekule declined and suggested the name of his first doctoral student, Adolf von Baeyer (Baeyer, Adolf von). Baeyer was later to receive one of the first Nobel Prizes; his teacher did not live long enough for that.

In 1890 the 25th anniversary of Kekule's first benzene paper was marked by an elaborate celebration in his honour. This was the occasion when he publicly related the stories that have since become well known, about how the ideas for structure theory and benzene theory came to him while daydreaming or dozing. The first of these events happened, he said, on the upper deck of a horse-drawn London omnibus (if true, it was probably in the summer of 1855). The second occurred in his residence in Ghent (perhaps in early 1862) and involved a dream figure of a snake that seized its own tail in its mouth, giving him the idea for the benzene ring. However, the precise dating of these dreams, and even their very existence, has been contested.

In contrast to his career success, Kekule's private life was unsettled. His first wife died giving birth to their first child, a son; a later marriage proved unhappy. The year before his death, he was raised to the hereditary Prussian nobility and adopted the aristocratic surname Kekule von Stradonitz.