Werner was born the son of an ironworker at Mulhouse in France. He was educated at the University of Zurich, where he gained his PhD in 1890. After a year in Paris working with Marcellin Berthelot he returned to Zurich, where he was appointed professor of chemistry in 1895.

In 1905 Werner produced a work, later translated into English as New Ideas on Inorganic Chemistry (1911), which was to revolutionize inorganic chemistry and earn him the Nobel Prize for chemistry in 1913. Although the ideas introduced by August Kekulé had contributed greatly to organic chemistry, attempts to apply his valence theory to inorganic molecules were much less successful. Many metals appeared to show variable valence and form complex compounds.

Werner proposed distinguishing between a primary and a secondary valence of a metal. The primary was concerned with binding ions, while the secondary valence applied not only to atoms but also to molecules, which can have an independent existence. Certain metals, such as cobalt and platinum, were capable through their secondary valences of joining to themselves a certain number of atoms or molecules. These were termed by Werner ‘coordination compounds’ and the maximum number of atoms (or ‘ligands’ as he called them) that can be joined to the central metal is its coordination number. This led Werner to make very detailed predictions about the existence of certain hitherto unsuspected isomers. He managed to resolve optical isomers of an inorganic compound in 1911.