Vauquelin was born at Saint-André-d'Hébertot in Normandy, France, the son of Nicolas Vauquelin, an estate manager, and his wife, Catherine Le Charterier.
His first acquaintance with chemistry was gained as laboratory assistant to an apothecary in Rouen (1777–1779), and after various vicissitudes he obtained an introduction to A. F. Fourcroy, in whose laboratory he was an assistant from 1783 to 1791.
Moving to Paris, he became a laboratory assistant at the Jardin du Roi and was befriended by a professor of chemistry. In 1791 he was made a member of the Academy of Sciences and from that time he helped to edit the journal Annales de Chimie (Chemical annals), although he left the country for a while during the height of the French Revolution. In 1798 Vauquelin discovered beryllium oxide by extracting it from an emerald (a beryl variety); Klaproth isolated the element from the oxide.